Tracking the immune response with single-cell genomics

The immune system is composed of a diverse array of cell types, each with a specialized role in orchestrating the immune response to pathogens or cancer. Even within a single cell ‘type,’ individual cells can access a wide spectrum of differentiation and activation states, which reflect the physiological response of each cell to the tissue environment and immune stimuli. Thus, the cellular diversity of the immune system is inherently quite complex and understanding this complexity has greatly benefited from technologies that measure immune responses at single-cell resolution, in addition to the systems-level response as a whole. In this Commentary, we focus on recent work at the interface of immunology and single-cell genomics and highlight advances in technologies and their application to immune cells. In particular, we highlight recent single-cell genomic profiling studies of T cells, since somatic rearrangements in the T cell receptor (TCR) loci enable the tracking of clonal T cell responses through space and time. Finally, we discuss opportunities for future use of these technologies in understanding vaccination and the basis for effective vaccine-induced immunity.     

Calibration weighted estimation of semiparametric transformation models for two‐phase sampling

Two‐phase designs are commonly used to subsample subjects from a cohort in order to study covariates that are too expensive to ascertain for everyone in the cohort. This is particularly true for the study of immune response biomarkers in vaccine immunology, where new, elaborate assays are constantly being developed to improve our understanding of the human immune responses to vaccines and how the immune response may protect humans from virus infection. It has long being recognized that if there exist variables that are correlated with expensive variables and can be measured for every subject in the cohort, they can be leveraged to improve the estimation efficiency for the effects of the expensive variables. In this research article, we developed an improved inverse probability weighted estimation approach for semiparametric transformation models with a two‐phase study design. Semiparametric transformation models are a class of models that include the Cox PH and proportional odds models. They provide an attractive way to model the effects of immune response biomarkers as human immune responses generally wane over time. Our approach is based on weights calibration, which has its origin in survey statistics and was used by Breslow et al. 1 , 2 to improve inverse probability weighted estimation of the Cox regression model. We develop asymptotic theory for our estimator and examine its performance through simulation studies. We illustrate the proposed method with application to two HIV‐1 vaccine efficacy trials. Copyright © 2015 John Wiley & Sons, Ltd.     

Analysis of cell-mediated immune responses in support of dengue vaccine development efforts

Dengue vaccine development has made significant strides, but a better understanding of how vaccine-induced immune responses correlate with vaccine efficacy can greatly accelerate development, testing, and deployment as well as ameliorate potential risks and safety concerns. Advances in basic immunology knowledge and techniques have already improved our understanding of cell-mediated immunity of natural dengue virus infection and vaccination. We conclude that the evidence base is adequate to argue for inclusion of assessments of cell-mediated immunity as part of clinical trials of dengue vaccines, although further research to identify useful correlates of protective immunity is needed.     

Formulation of the respiratory syncytial virus fusion protein with a polymer-based combination adjuvant promotes transient and local innate immune responses and leads to improved adaptive immunity

Respiratory syncytial virus (RSV) causes serious upper and lower respiratory tract infections in newborns and infants. Presently, there is no licensed vaccine against RSV. We previously reported the safety and efficacy of a novel vaccine candidate (ΔF/TriAdj) in rodent and lamb models following intranasal immunization. However, the effects of the vaccine on the innate immune system in the upper and lower respiratory tracts, when delivered intranasally, have not been characterized. In the present study, we found that ΔF/TriAdj triggered transient production of chemokines, cytokines and interferons in the nasal tissues and lungs of BALB/c mice. The types of chemokines produced were consistent with the populations of immune cells recruited, i.e. dendritic cells, macrophages and neutrophils, in the nose-associated lymphoid tissue (NALT), lung and their draining lymph nodes of the ΔF/TriAdj-immunized group. In addition, ΔF/TriAdj stimulated cellular activation with generation of mucosal and systemic antibody responses, and conferred complete protection from viral infection in the lungs upon RSV challenge. The effect of ΔF/TriAdj was short-lived in the nasal tissues and more prolonged in the lungs. In addition, both innate and adaptive immune responses were lower when mice were immunized with ΔF alone. These results suggest that ΔF/TriAdj modulates the innate mucosal environment in both upper and lower respiratory tracts, which contributes to robust adaptive immune responses and long-term protective efficacy of this novel vaccine formulation.     

DNA vaccines encoding altered peptide ligands for SSX2 enhance epitope-specific CD8+ T-cell immune responses

Plasmid DNA serves as a simple and easily modifiable form of antigen delivery for vaccines. The USDA approval of DNA vaccines for several non-human diseases underscores the potential of this type of antigen delivery method as a cost-effective approach for the treatment or prevention of human diseases, including cancer. However, while DNA vaccines have demonstrated safety and immunological effect in early phase clinical trials, they have not consistently elicited robust anti-tumor responses. Hence many recent efforts have sought to increase the immunological efficacy of DNA vaccines, and we have specifically evaluated several target antigens encoded by DNA vaccine as treatments for human prostate cancer. In particular, we have focused on SSX2 as one potential target antigen, given its frequent expression in metastatic prostate cancer. We have previously identified two peptides, p41-49 and p103-111, as HLA-A2-restricted SSX2-specific epitopes. In the present study we sought to determine whether the efficacy of a DNA vaccine could be enhanced by an altered peptide ligand (APL) strategy wherein modifications were made to anchor residues of these epitopes to enhance or ablate their binding to HLA-A2. A DNA vaccine encoding APL modified to increase epitope binding elicited robust peptide-specific CD8+ T cells producing Th1 cytokines specific for each epitope. Ablation of one epitope in a DNA vaccine did not enhance immune responses to the other epitope. These results demonstrate that APL encoded by a DNA vaccine can be used to elicit increased numbers of antigen-specific T cells specific for multiple epitopes simultaneously, and suggest this could be a general approach to improve the immunogenicity of DNA vaccines encoding tumor antigens.     

Efficacy and functionality of lipoprotein OprI from Pseudomonas aeruginosa as adjuvant for a subunit vaccine against classical swine fever

Bacterial lipoproteins are potent stimulators of innate immune responses and can mediate humoral and cytotoxic T cell responses without additional adjuvants. OprI derived from Pseudomonas aeruginosa was tested in vitro and in vivo for its adjuvant potential in the context of a classical swine fever (CSF) subunit vaccine. OprI activated porcine monocyte-derived dendritic cells (MoDC), upregulating CD80/86 and MHC class II expression, as well as pro-inflammatory cytokines. OprI enhanced CSFV-antigen-specific lymphocyte proliferation and IFN-gamma release. An E2/NS3-based subunit vaccine adjuvanted with OprI stimulated specific immune responses and partial protection against CSFV infection. Although, a water-oil-water adjuvanted vaccine was more potent at protecting animals, this study demonstrates that OprI has immunostimulatory properties for porcine DC, and has potential as vaccine immunostimulant. Further studies are necessary to optimize antigen formulation enabling to translate the in vitro efficacy into a potent vaccine in vivo.     

Modular platforms for the assembly of self-adjuvanting lipopeptide-based vaccines for use in an out-bred population

To facilitate the preparation of synthetic epitope-based self-adjuvanting vaccines capable of eliciting antibody responses in an out-bred population, we have developed two modular approaches. In the first, the Toll-like receptor 2 agonist Pam₂Cys and the target antibody epitope are assembled as a module which is then coupled to a carrier protein as a source of antigens to stimulate T cell help. A vaccine candidate made in this way was shown to induce a specific immune response in four different strains of mice without the need for extraneous adjuvant. In the second approach, three vaccine components in the form of a target antibody epitope, a T helper cell epitope and Pam₂Cys, were prepared separately each carrying different chemical functional groups. By using pH-mediated chemo-selective ligations, the vaccine was assembled in a one-pot procedure. Using this approach, a number of vaccine constructs including a lipopeptide-protein conjugate were made and also shown to elicit immune responses in different strains of mice. These two modular approaches thus constitute a powerful platform for the assembly of self-adjuvanting lipopeptide-based vaccines that can potentially be used to induce robust antibody responses in an outbred population. Finally, our study of the impact of chemical linkages on immunogenicity of a lipopeptide vaccine shows that a stable covalent bond between Pam2Cys and a B cell epitope, rather than between Pam2Cys and T helper cell epitope is critical for the induction of antibody responses and biological efficacy, indicating that Pam2Cys functions not only as an adjuvant but also participates in processing and presentation of the immunogen.     

Utilization of gut environment-mediated control system of host immunity in the development of vaccine adjuvants

Vaccination is one of the most powerful strategies for the preventive and therapeutic control of infectious diseases and other diseases such as cancer. To maximize the effectiveness of vaccines, it is necessary to modify the immune responses by means of adjuvants. The gut environment, including commensal bacteria and dietary components, has been proven to be able to mediate host immunity. An understanding of gut microbiota–related regulation of immune responses has revealed the potential adjuvanticity of particular microbiota-derived compounds, driving exploration into their development as vaccine adjuvants. In this review, we discuss how commensal bacteria and compounds derived from them regulate host immune responses, and we propose the potential application of these compounds as vaccine adjuvants.     

How advances in immunology provide insight into improving vaccine efficacy

Vaccines represent one of the most compelling examples of how biomedical research has improved society by saving lives and dramatically reducing the burden of infectious disease. Despite the importance of vaccinology, we are still in the early stages of understanding how the best vaccines work and how we can achieve better protective efficacy through improved vaccine design. Most successful vaccines have been developed empirically, but recent advances in immunology are beginning to shed new light on the mechanisms of vaccine-mediated protection and development of long-term immunity. Although natural infection will often elicit lifelong immunity, almost all current vaccines require booster vaccination in order to achieve durable protective humoral immune responses, regardless of whether the vaccine is based on infection with replicating live-attenuated vaccine strains of the specific pathogen or whether they are derived from immunization with inactivated, non-replicating vaccines or subunit vaccines. The form of the vaccine antigen (e.g., soluble or particulate/aggregate) appears to play an important role in determining immunogenicity and the interactions between dendritic cells, B cells and T cells in the germinal center are likely to dictate the magnitude and duration of protective immunity. By learning how to optimize these interactions, we may be able to elicit more effective and long-lived immunity with fewer vaccinations.     

Protective efficacy of a tandemly linked,multi-subunit recombinant leishmanial vaccine (Leish-111f) formulated in MPL adjuvant

Three immunodominant leishmanial antigens (TSA, LmSTI1 and LeIF) previously identified in the context of host response to infection in infected donors and BALB/c mice, as well as their ability to elicit at least partial protection against Leishmania major infection in the BALB/c mouse model, were selected for inclusion into a subunit based vaccine. This is based on the premise that an effective vaccine against leishmaniasis (a complex parasitic infection) would require a multivalent cocktail of several antigens containing a broader range of protective epitopes that would cover a wide range of MHC types in a heterogeneous population. For practical considerations of vaccine development, we report on the generation of a single recombinant polyprotein comprising the sequences of all three open reading frames genetically linked in tandem. The resulting molecule, Leish-111f, comprises an open reading frame that codes for a 111kDa polypeptide. Evaluation of the immunogenicity and protective efficacy of Leish-111f formulated with IL-12 revealed that the immune responses to the individual components were maintained and as well, rLeish-111f protected BALB/c mice against L. major infection to a magnitude equal or superior to those seen with any of the individual components of the vaccine construct or SLA, a soluble Leishmania lysate. But because rIL-12 is expensive and difficult to manufacture and its efficacy and safety as an adjuvant for human use is questionable, we screened for other adjuvants that could potentially substitute for IL-12. We report that monophosphoryl lipid A (MPL) plus squalene (MPL-SE) formulated with rLeish-111f elicited protective immunity against L. major infection. The demonstrated feasibility to manufacture a single recombinant vaccine comprising multiple protective open reading frames and the potential use of MPL-SE as a substitute for IL-12, takes us closer to the realization of an affordable and safe Leishmania vaccine.     

Towards new immunotherapies: targeting recombinant cytokines to the immune system using live attenuated Salmonella

We have used Salmonella as a delivery system for eukaryotic expression plasmids encoding cytokines, and assessed its capacity to modulate immune responses in different experimental models. Plasmids encoding mouse IL-4 and IL-18 under cytomegalovirus promoter were constructed and transformed into live attenuated Salmonella enterica serovar Typhi strain CVD 908-htrA, and Salmonella enterica serovar Typhimurium strain SL3261. We have shown that systemic as well as mucosal immunization with such constructs can influence the antibody and cytokine responses to the Salmonella carrier and to co-administered bystander antigens, as well as the specific immune response elicited during a parasitic infection. Further, we have shown that oral cytokine-therapy using Salmonella as gene vector induce antitumoral effect as demonstrated by extended survival time in melanoma-bearing mice.This approach may be particularly suited for the development of new immunotherapies with applications in parasitic infections and cancer, were alterations of the host's immune responses are usually found, and therapy-induced modulation of the immune response is likely to be required.     

Prediction of pertussis vaccine efficacy using a correlates of protection model

A previously developed statistical model relates vaccine immune responses to protection against pertussis disease in a household contact setting. Before this model can be used to predict the risk of disease based on immune responses, it must be validated to demonstrate reliable predictions. The model is shown here to be validated in terms of statistical criteria (Prentice surrogacy measures) as well as predictive capability in an independent efficacy trial (meta-analysis). Additionally, the model is used to predict efficacy from two recent immunogenicity trials comparing a 5-component acellular pertussis pentavalent combination vaccine with separate administration of its vaccine components. The model predicted similar protective efficacy rates: 82% after three doses and 83% after four doses. Follow-up of these subjects the model also predicted sustained and comparable efficacy for the combination and separate vaccines (75%) up to the pre-school booster age.     

Immunobiology of dendritic cells and their application in clinical practice

INTRODUCTION: Dendritic cells play a central role in the regulation of the immune responses towards cellular or humoral immunity. Several types of dendritic cells can be distinguished, which originate from different hematopoietic lineages, and differ from each other in function, morphology and localization within the organism. Immature dendritic cell-precursors originate from bone marrow haemopoietic stem cells, circulate in blood system and reach peripheral tissues, where they differentiate into active antigen capturing and processing cells. They have further maturation by the effect of adequate signals (antigen stimuli and inflammatory cytokines) and migrate into secondary lymphoid organs, presented cell surface MHC molecules-linked peptides from antigens which they have captured and processed, to T lymphocytes, induce immune reaction by T cell activation. Apart from the fact that dendritic cells as professional antigen presenting cells are essential to induction T cell-mediated immune responses, they influence activation and function of B lymphocytes and effector cells of natural immune system by cytokines and cell-cell interactions. CONCLUSIONS: Complex regulatory function of dendritic cells make a possibility for artificial alteration of immune processes by modification of dendritic cells: direct against definitive antigens, increase or decrease their intensity, hereby we can accomplish the immunotherapy of different diseases such as tumors, infection, autoimmune diseases, transplants' rejection.     

Modulation of immunosuppressant drug treatment to improve SARS-CoV-2 vaccine efficacy in mice

The COVID-19 pandemic dramatically demonstrated the need for improved vaccination strategies and therapeutic responses to combat infectious diseases. However, the efficacy of vaccines has not yet been demonstrated in combination with commonly used immunosuppressive drug regimens. We sought to determine how common pharmaceutical drugs used in autoimmune disorders can alter immune responses to the SARS-CoV-2 spike protein vaccination. We treated mice with five immunosuppressant drugs (cyclophosphamide, leflunomide, methotrexate, methylprednisolone, and mycophenolate mofetil), each with various mechanisms of action prior to and following immunization with SARS-CoV-2 spike protein. We assessed the functionality of antibody responses to spike protein and compared immune cell populations in mice that received no treatment with those that received continuous or temporarily suspended immune suppressive therapy. All tested immunosuppressants significantly reduced the antibody titers in serum and functional antibody response against SARS-CoV-2 spike protein in immunized mice. Temporarily halting selected immunosuppressants (methylprednisolone and methotrexate, but not cyclophosphamide) improved antibody responses significantly. Through proof-of-principle experiments utilizing a mouse model, we demonstrated that immune suppression in autoimmune disorders through pharmaceutical treatments may impair vaccine response to SARS-CoV-2, and temporary suspension of immunosuppressant treatment may be necessary to mount an effective antibody vaccine response. This work provides feasibility for future clinical assessment of the impact of immunosuppressants on vaccine efficacy in humans.     

The role of mass spectrometry in vaccine development

For the most part, vaccine development to date has been empiric. While sometimes successful, such a strategy is 'hit or miss', and fails to advance the basic science of vaccine development. Preferable would be tools that allow for a more directed development of vaccines at either the population or sub-population level. Characteristics of useful tools in vaccine development should include the ability to identify and characterize the spectrum of antigenic peptides presented by MHC molecules to which the immune system responds by the development of protective immune responses. In addition, because the explosion in human genomics allows the ability to understand MHC haplotypes at the population level, as well as an enhanced understanding of MHC binding motifs, new tools might further allow for an understanding of which vaccine antigens are capable of being bound and presented to the immune system by MHC molecules. New mass spectrometry technology fulfils these criteria, and may well lead to a revolution in the design of new vaccines. This paper will review the basics of mass spectrometry techniques as applied to the identification and characterization of vaccine peptide antigens, and discusses how these tools can be applied to vaccine development.     

Evaluation of immune response to single dose of quadrivalent HPV vaccine at 10-year post-vaccination

BackgroundThe recent World Health Organization recommendation supporting single-dose of HPV vaccine will significantly reduce programmatic cost, mitigate the supply shortage, and simplify logistics, thus allowing more low- and middle-income countries to introduce the vaccine. From a programmatic perspective the durability of protection offered by a single-dose will be a key consideration. The primary objectives of the present study were to determine whether recipients of a single-dose of quadrivalent HPV vaccine had sustained immune response against targeted HPV types (HPV 6,11,16,18) at 10 years post-vaccination and whether this response was superior to the natural antibody titres observed in unvaccinated women.MethodsParticipants received at age 10–18 years either one, two or three doses of the quadrivalent HPV vaccine. Serology samples were obtained at different timepoints up to 10 years after vaccination from a convenience sample of vaccinated participants and from age-matched unvaccinated women at one timepoint. The evolution of the binding and neutralizing antibody response was presented by dose received. 10-year durability of immune responses induced by a single-dose was compared to that after three doses of the vaccine and in unvaccinated married women.ResultsThe dynamics of antibody response among the single-dose recipients observed over 120 months show stabilized levels 18 months after vaccination for all four HPV types. Although the HPV type-specific (binding or neutralizing) antibody titres after a single-dose were significantly inferior to those after three doses of the vaccine (lower bounds of GMT ratios < 0.5), they were all significantly higher than those observed in unvaccinated women following natural infections (GMT ratios: 2.05 to 4.04-fold higher). The results correlate well with the high vaccine efficacy of single-dose against persistent HPV 16/18 infections reported by us earlier at 10-years post-vaccination.ConclusionOur study demonstrates the high and durable immune response in single-dose recipients of HPV vaccine at 10-years post vaccination.     

Enhancement of protein vaccine potency by in vivo electroporation mediated intramuscular injection

Protein-based vaccines have emerged as a potentially promising approach for the generation of antigen-specific immune responses. However, due to their low immunogenicity, there is a need for innovative approaches to enhance protein-based vaccine potency. One approach to enhance protein-based vaccine potency is the employment of toll-like receptor ligands, such as CpG oligonucleotides, to activate the antigen-specific T cell immune responses. Another approach involves employing a method capable of improving the delivery of protein-based vaccine intramuscularly to lead to the slow release of the protein, resulting in improved vaccine potency. In the current study, we aimed to determine whether intramuscular injection of protein-based vaccines in conjunction with CpG followed by electroporation can lead to increased delivery of the protein-based vaccine into muscle cells, resulting in enhanced protein-based vaccine potency. We found that intramuscular injection followed by electroporation can effectively transduce the protein-based vaccine into the muscle cells. Furthermore, we found that intramuscular vaccination with OVA protein in combination with CpG followed by electroporation generates the best OVA-specific CD8+ T cell immune responses as well as the best protective and therapeutic antitumor effects in vaccinated mice. CD8+ T cells were found to play an important role in the observed protective antitumor effects generated by the vaccination. Similar results were observed using the HPV-16 E7 protein-based vaccination system. Thus, our data indicate that intramuscular administration of protein-based vaccines in conjunction with CpG followed by electroporation can significantly enhance the antigen-specific CD8+ T cell immune responses. The clinical implications of the study are discussed.