Both Humoral and Cellular Immunity Limit the Ability of Live Attenuated Influenza Vaccines to Promote T Cell Responses

One potential advantage of live attenuated influenza vaccines (LAIVs) is their ability to establish both virus-specific Ab and tissue-resident memory T cells (TRM) in the respiratory mucosa. However, it is hypothesized that pre-existing immunity from past infections and/or immunizations prevents LAIV from boosting or generating de novo CD8+ T cell responses. To determine whether we can overcome this limitation, we generated a series of drifted influenza A/PR8 LAIVs with successive mutations in the hemagglutinin protein, allowing for increasing levels of escape from pre-existing Ab. We also inserted a CD8+ T cell epitope from the Sendai virus nucleoprotein (NP) to assess both generation of a de novo T cell response and boosting of pre-existing influenza-specific CD8+ T cells following LAIV immunization. Increasing the level of escape from Ab enabled boosting of pre-existing TRM, but we were unable to generate de novo Sendai virus NP+ CD8+ TRM following LAIV immunization in PR8 influenza-immune mice, even with LAIV strains that can fully escape pre-existing Ab. As these data suggested a role for cell-mediated immunity in limiting LAIV efficacy, we investigated several scenarios to assess the impact of pre-existing LAIV-specific TRM in the upper and lower respiratory tract. Ultimately, we found that deletion of the immunodominant influenza NP366-374 epitope allowed for sufficient escape from cellular immunity to establish de novo CD8+ TRM. When combined, these studies demonstrate that both pre-existing humoral and cellular immunity can limit the effectiveness of LAIV, which is an important consideration for future design of vaccine vectors against respiratory pathogens.

Persistent Antigen Harbored by Alveolar Macrophages Enhances the Maintenance of Lung-Resident Memory CD8+ T Cells

Lung tissue-resident memory T cells are crucial mediators of cellular immunity against respiratory viruses; however, their gradual decline hinders the development of T cell-based vaccines against respiratory pathogens. Recently, studies using adenovirus (Ad)-based vaccine vectors have shown that the number of protective lung-resident CD8+ TRMs can be maintained long term. In this article, we show that immunization of mice with a replication-deficient Ad serotype 5 expressing influenza (A/Puerto Rico/8/34) nucleoprotein (AdNP) generates a long-lived lung TRM pool that is transcriptionally indistinct from those generated during a primary influenza infection. In addition, we demonstrate that CD4+ T cells contribute to the long-term maintenance of AdNP-induced CD8+ TRMs. Using a lineage tracing approach, we identify alveolar macrophages as a cell source of persistent NP Ag after immunization with AdNP. Importantly, depletion of alveolar macrophages after AdNP immunization resulted in significantly reduced numbers of NP-specific CD8+ TRMs in the lungs and airways. Combined, our results provide further insight to the mechanisms governing the enhanced longevity of Ag-specific CD8+ lung TRMs observed after immunization with recombinant Ad.

Human lung tissue-resident memory CD8+ T cells are transcriptionally, epigenetically, and phenotypically diverse

Tissue-resident memory CD8+ T cells (TRM) are strategically located in peripheral tissues, especially at mucosal surfaces, where they can provide protection against invading pathogenic microbes. In the lungs, TRM play a critical role in limiting disease and transmission of respiratory viruses; however, the heterogeneity present in TRM populations in the human lung remains largely unexplored. Here we show that human lungs harbor transcriptionally, epigenetically, and phenotypically distinct populations of memory CD8+ T cells expressing the tissue residency-associated markers CD69 and CD103. High-dimensional flow cytometry and single-cell RNA sequencing of memory CD8+ T cells isolated from human lungs shows that heterogeneity exists both between and within CD69+ CD103− and CD69+ CD103+ subsets, with transcriptional diversity among the CD69+ CD103− subset being most prominent. Single-cell ATACseq demonstrates that similar levels of epigenetic diversity exist between and within these different TRM subsets. However, flow cytometry and single-cell RNAseq of influenza- and SARS-CoV-2-specific lung TRM demonstrates that heterogeneity between CD69+ CD103− and CD69+ CD103+ subsets is largely eliminated when the cells are specific for a common antigen. Together, these data illuminate underappreciated and unexplored aspects of heterogeneity in TRM populations in humans.

Supported by grants from NIH/NIAID (75N93019R00028) and NIH/NHLBI (R35 HL150803)

Examining effector functions of lung CD8+ tissue resident memory T cells in humans

Due to their position in the lung tissue, CD8+ tissue resident memory T cells (TRM) act as sentinels of the respiratory tract that rapidly respond to, and mediate protection against, respiratory viruses. In mice, TRM have been shown to mediate protection at barrier sites by producing cytokines, chemokines, and performing cell lysis. In the lungs specifically, our lab has shown that influenza-specific CD8+ TRM rapidly produce IFNγ, but airway TRM are poorly cytolytic in mice. In humans, less is known about the effector functions of virus-specific CD8+ TRM in the lungs, and thus this study seeks to fill that gap in knowledge. Using cells from healthy human lungs, we first identified and quantified the frequency of antigen-specific cells in our lung donors by performing intracellular cytokine staining (IFNγ+) and activation induced marker assays (CD137+ CD25+). Then, by performing a series of in vitro peptide stimulation and cytokine neutralization experiments, we investigated which cytokines are produced by lung CD8+ TRM, and how those cytokines impact local innate and epithelial cells. Initial results show that, when stimulated with their cognate antigen, lung CD8+ TRM produce cytokines that directly activate innate immune cells. Results of this study suggests that human CD8+ TRM in the lungs act to rapidly reprogram local immune cells, and these data will ultimately help us understand how CD8+ TRM fit into the overall immune response to respiratory viruses.

Supported by grants from the NIH/NHLBI (R35 HL150803) and by NIH/NIAD through the Centers of Excellence for Influenza Research and Response (75N93019R00028).

Impact of pre-existing immunity on the development of de novo virus-specific TRM following live attenuated influenza vaccination

Live attenuated influenza vaccine (LAIV) elicits both humoral and cellular immune memory in children, but its efficacy is limited in adults. We hypothesize that pre-existing immunity from past infections and/or immunizations prevents the attenuated vaccine from establishing an immune response. To determine if we can overcome this limitation by increasing the antigenic distance of the vaccine strain from previous circulating seasonal strains, we generated a series of drifted LAIVs with successive mutations in the HA protein, allowing for increasing levels of escape from pre-existing antibody. We also inserted a CD8+ T cell epitope from the Sendai virus nucleoprotein (SeV-NP) as a readout for generation of a de novo TRM response following immunization. Surprisingly, we were unable to identify SeV-NP+ CD8+ TRM following LAIV immunization in PR8-immune mice, even with LAIV strains that can fully escape pre-existing antibody. As these data suggested a role for cell-mediated immunity in limiting LAIV efficacy, we investigated several scenarios to assess the impact of pre-existing LAIV-specific TRM in the upper and lower respiratory tract. Ultimately, we found that deletion of the immunodominant influenza NP366–374 epitope was sufficient to escape pre-existing CD8+ TRM and to establish de novo CD8+ TRM. Combined, these studies demonstrate that both pre-existing humoral and cellular immunity can limit the effectiveness of LAIV, thereby informing future design of vaccine vectors against respiratory pathogens.

Supported by grants from NIH (F31 HL156639-01, R35 HL150803)

Lineage analysis defines subpopulations of human lung tissue-resident memory CD8+ T cells

Tissue resident memory T cells (TRM) are important for local immunity and recall responses. In contrast to effector and central memory T cells, TRM remain in the tissues and do not circulate throughout the body. CD69 and CD103 expression are distinguishing markers of TRM cells, although TRM cells expressing only one marker, or absent of both markers, have been described, suggesting further heterogeneity beyond these markers. Many of the phenotypic characteristics and transcriptional properties of TRM cells have been defined in animal models, where in vivo labeling can be used to define tissue residency. Therefore, a deeper understanding of what defines human TRM cells and their molecular heterogeneity is necessary. To address this, single-cell multi-omics data of memory CD8+ T cells isolated from human lungs that have been phenotypically subsetted into CD69+, CD69+CD103+, CD69-CD103-, and naive cells were collected and analyzed by scATAC-seq and scRNA-seq approaches. A lineage analysis of these data identified multiple distinct lineages of TRM cells in human lungs. From this, we defined the genes that drive each lineage through their differentiation program, the variable transcription factor motifs that distinguish each lineage terminal state, and estimate the rate of differentiation as the cells transition. In identifying these subpopulations, we can begin to understand the heterogeneity of TRM cells in humans on a molecular level.

Supported by a grant from the NIH/NIAID (75N93019R00028) and a grant from the NIH/NHLBI (R35 HL150803)

Identifying mechanisms that enhance the longevity of tissue-resident memory CD8+ T cells in the lung

Lung tissue-resident memory CD8+ T cells (TRM) are crucial mediators of cellular immunity against influenza viruses, but the number of these cells in the lung tissue gradually declines in the months following influenza infection. Recently, we showed that intranasal immunization with a replication-deficient adenovirus that expresses the nucleoprotein from influenza A virus (AdNP) results in long-term maintenance of lung CD8+ TRM for up to 1-year post-immunization. However, the mechanism(s) that promote this enhanced longevity of FluNP-specific CD8+ lung TRM remain unknown. Using a combination of mouse infection models, flow cytometry, and RNA-sequencing, we compared CD8+ T cells from the airways, lungs, and spleen of AdNP-immunized or influenza x31-infected mice. We found that CD8+ TRM in the lungs of AdNP-immunized mice show increased homeostatic turnover and hallmarks of persistent antigen stimulation in the lung. However, RNA-sequencing analysis comparing lung CD8+ TRM from AdNP-immunized and x31-infected mice at 1-month and 1-year post-immunization showed only minor variations that did not fully explain the differences in lung TRM persistence. Lineage tracing experiments using a Cre recombinase-expressing Adenovirus (AdCre) identified alveolar macrophages as the primary cell type harboring persistent antigen in the lung. Together, these results define one mechanism for enhancing the durability of lung TRM, which is an important consideration for the design of future cell-mediated influenza vaccines

Identifying mechanisms that enhance the longevity of tissue-resident memory T cells in the lung

Lung tissue-resident memory T cells (TRM) are crucial mediators of cellular immunity against influenza viruses, but the number of these cells in the lung tissue gradually declines in the months following influenza infection. Recently, we showed that intranasal immunization with a replication-deficient Adenovirus that expresses the nucleoprotein from influenza A virus (AdNP) results in long-term maintenance of lung CD8+ TRM for up to 1-year post-immunization. However, the mechanism(s) that promote this enhanced longevity of CD8+ lung TRM remain unknown. Using a combination of mouse infection models, flow cytometry, and RNA-sequencing, we compared CD8+ T cells from the airways, lung, and spleen from AdNP-immunized or influenza x31-infected mice. We found that CD8+ TRM in the lungs of AdNP-immunized mice show increased homeostatic turnover and encounter persistent antigen in the lung. In addition, parabiosis experiments suggest that the influenza-specific CD8+ lung TRM pool is maintained in AdNP-immunized mice by continual recruitment of circulating TEM into the lung TRM pool. RNA-sequencing analysis comparing CD8+ lung TRM from AdNP-immunized and x31-infected mice at 1-month and 1-year post-immunization showed only minor variations that did not fully explain the differences in lung TRM persistence. We are currently investigating how antigen is maintained in the lung following AdNP immunization using microscopy and Cre recombinase-expressing Adenovirus (AdCre) to identify antigen presenting cells harboring antigen long-term in the lung. The results of this study will identify mechanisms that improve the durability of cellular immunity, and will thus inform future design of cell-mediated influenza vaccines.

The Human Lung Glycome Reveals Novel Glycan Ligands for Influenza A Virus

Glycans within human lungs are recognized by many pathogens such as influenza A virus (IAV), yet little is known about their structures. Here we present the first analysis of the N- and O- and glycosphingolipid-glycans from total human lungs, along with histological analyses of IAV binding. The N-glycome of human lung contains extremely large complex-type N-glycans with linear poly-N-acetyllactosamine (PL) [-3Galβ1-4GlcNAcβ1-]n extensions, which are predominantly terminated in α2,3-linked sialic acid. By contrast, smaller N-glycans lack PL and are enriched in α2,6-linked sialic acids. In addition, we observed large glycosphingolipid (GSL)-glycans, which also consists of linear PL, terminating in mainly α2,3-linked sialic acid. Histological staining revealed that IAV binds to sialylated and non-sialylated glycans and binding is not concordant with respect to binding by sialic acid-specific lectins. These results extend our understanding of the types of glycans that may serve as binding sites for human lung pathogens.

LSD1 Cooperates with Noncanonical NF-κB Signaling to Regulate Marginal Zone B Cell Development

Marginal zone B cells (MZB) are a mature B cell subset that rapidly respond to blood-borne pathogens. Although the transcriptional changes that occur throughout MZB development are known, the corresponding epigenetic changes and epigenetic modifying proteins that facilitate these changes are poorly understood. The histone demethylase LSD1 is an epigenetic modifier that promotes plasmablast formation, but its role in B cell development has not been explored. In this study, a role for LSD1 in the development of B cell subsets was examined. B cell-conditional deletion of LSD1 in mice resulted in a decrease in MZB whereas follicular B cells and bone marrow B cell populations were minimally affected. LSD1 repressed genes in MZB that were normally upregulated in the myeloid and follicular B cell lineages. Correspondingly, LSD1 regulated chromatin accessibility at the motifs of transcription factors known to regulate splenic B cell development, including NF-κB motifs. The importance of NF-κB signaling was examined through an ex vivo MZB development assay, which showed that both LSD1-deficient and NF-κB-inhibited transitional B cells failed to undergo full MZB development. Gene expression and chromatin accessibility analyses of in vivo- and ex vivo-generated LSD1-deficient MZB indicated that LSD1 regulated the downstream target genes of noncanonical NF-κB signaling. Additionally LSD1 was found to interact with the noncanonical NF-κB transcription factor p52. Together, these data reveal that the epigenetic modulation of the noncanonical NF-κB signaling pathway by LSD1 is an essential process during the development of MZB.

Unrelated respiratory infections compromise established cellular immunity by promoting apoptosis of pre-existing lung-resident memory CD8 T cells

Lung-resident memory T cells (lung TRM) are critical for protective heterosubtypic immunity against influenza viruses. However, the efficacy of cellular immunity against respiratory pathogens such as influenza wanes over time due to the gradual loss of flu-specific lung TRM. One possible mechanism for this decline is frequent exposure to environmental and biological insults resulting in localized inflammation that promotes the death of established lung TRM. We investigated whether unrelated infections could exacerbate the loss of pre-existing, flu-specific lung TRM and reduce the efficacy of cellular immunity to subsequent influenza challenge. Infection of influenza-immune mice with Sendai virus, an unrelated murine parainfluenza virus, resulted in significantly higher viral titers and greater morbidity following influenza challenge compared to PBS-treated controls. This loss of protective cellular immunity corresponded to a significant decrease in the number of pre-existing flu-specific lung CD8 TRM compared to PBS controls due to increased apoptosis. This loss of pre-existing lung TRM following Sendai infection was not due to competition for limited resources or tissue niches between flu- and Sendai-specific lung TRM. Sendai infection had no impact on the number of systemic flu-specific memory CD8 T cells in the spleen. The loss of lung TRM required a respiratory infection, as LCMV infection and intranasal delivery of TLR agonists did not significantly reduce the number of pre-existing flu-specific lung CD8 TRM. Together, these data suggest that tissue damage induced by unrelated respiratory infections can promote the loss of pre-existing lung TRM and compromise cellular immunity against respiratory pathogens.

Nucleoside-modified mRNA vaccines induce potent T follicular helper and germinal center B cell responses

T follicular helper (Tfh) cells are required to develop germinal center (GC) responses and drive immunoglobulin class switch, affinity maturation, and long-term B cell memory. In this study, we characterize a recently developed vaccine platform, nucleoside-modified, purified mRNA encapsulated in lipid nanoparticles (mRNA-LNPs), that induces high levels of Tfh and GC B cells. Intradermal vaccination with nucleoside-modified mRNA-LNPs encoding various viral surface antigens elicited polyfunctional, antigen-specific, CD4⁺ T cell responses and potent neutralizing antibody responses in mice and nonhuman primates. Importantly, the strong antigen-specific Tfh cell response and high numbers of GC B cells and plasma cells were associated with long-lived and high-affinity neutralizing antibodies and durable protection. Comparative studies demonstrated that nucleoside-modified mRNA-LNP vaccines outperformed adjuvanted protein and inactivated virus vaccines and pathogen infection. The incorporation of noninflammatory, modified nucleosides in the mRNA is required for the production of large amounts of antigen and for robust immune responses.