Viral T-cell epitopes – Identification,characterization and clinical application

T-cell immunity, mediated by CD4⁺ and CD8⁺ T cells, represents a cornerstone in the control of viral infections. Virus-derived T-cell epitopes are represented by human leukocyte antigen (HLA)-presented viral peptides on the surface of virus-infected cells. They are the prerequisite for the recognition of infected cells by T cells. Knowledge of viral T-cell epitopes provides on the one hand a diagnostic tool to decipher protective T-cell immune responses in the human population and on the other hand various prophylactic and therapeutic options including vaccination approaches and the transfer of virus-specific T cells. Such approaches have already been proven to be effective against various viral infections, particularly in immunocompromised patients lacking sufficient humoral, antibody-based immune response. This review provides an overview on the state of the art as well as current studies regarding the identification and characterization of viral T-cell epitopes and approaches of clinical application. In the first chapter in silico prediction tools and direct, mass spectrometry-based identification of viral T-cell epitopes is compared. The second chapter provides an overview of commonly used assays for further characterization of T-cell responses and phenotypes. The final chapter presents an overview of clinical application of viral T-cell epitopes with a focus on human immunodeficiency virus (HIV), human cytomegalovirus (HCMV) and severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), being representatives of relevant viruses.     

Lung niches for the generation and maintenance of tissue-resident memory T cells

The extent to which tissue-specific viral infections generate memory T cells specifically adapted to and maintained within the target infection site is unknown. Here, we show that respiratory virus-specific memory T cells in mice and humans are generated and maintained in compartmentalized niches in lungs, distinct from populations in lymphoid tissue or circulation. Using a polyclonal mouse model of influenza infection combined with an in vivo antibody labeling approach and confocal imaging, we identify a spatially distinct niche in the lung where influenza-specific T-cell responses are expanded and maintained long term as tissue-resident memory (T_RM) CD4 and CD8 T cells. Lung T_RM are further distinguished from circulating memory subsets in lung and spleen based on CD69 expression and persistence independent of lymphoid stores. In humans, influenza-specific T cells are enriched within the lung T_RM subset, whereas memory CD8 T cells specific for the systemic virus cytomegalovirus are distributed in both lung and spleen, suggesting that the site of infection affects T_RM generation. Our findings reveal a precise spatial organization to virus-specific T-cell memory, determined by the site of the initial infection, with important implications for the development of targeted strategies to boost immunity at appropriate tissue sites.     

Distinct CD4 T-cell effects on primary versus recall CD8 T-cell responses during viral encephalomyelitis

CD4 T-cell help is not a universal requirement for effective primary CD8 T cells but is essential to generate memory CD8 T cells capable of recall responses. This study examined how CD4 T cells affect primary and secondary anti-viral CD8 T-cell responses within the central nervous system (CNS) during encephalomyelitis induced by sublethal gliatropic coronavirus. CD4 T-cell depletion before infection did not impair peripheral expansion, interferon-γ production, CNS recruitment or initial CNS effector capacity of virus-specific CD8 T cells ex vivo. Nevertheless, impaired virus control in the absence of CD4 T cells was associated with gradually diminished CNS CD8 T-cell interferon-γ production. Furthermore, within the CD8 T-cell population short-lived effector cells were increased and memory precursor effector cells were significantly decreased, consistent with higher T-cell turnover. Transfer of memory CD8 T cells to reduce viral load in CD4-depleted mice reverted the recipient CNS CD8 T-cell phenotype to that in wild-type control mice. However, memory CD8 T cells primed without CD4 T cells and transferred into infected CD4-sufficient recipients expanded less efficiently and were not sustained in the CNS, contrasting with their helped counterparts. These data suggest that CD4 T cells are dispensable for initial expansion, CNS recruitment and differentiation of primary resident memory CD8 T cells as long as the duration of antigen exposure is limited. By contrast, CD4 T cells are essential to prolong primary CD8 T-cell function in the CNS and imprint memory CD8 T cells for recall responses.     

The avidity of cross-reactive virus-specific T cells for their viral and allogeneic epitopes is variable and depends on epitope expression

Virus-specific T cells can recognize allogeneic HLA (allo-HLA) through cross-reactivity of their T-cell receptor (TCR). In a transplantation setting, such allo-HLA cross-reactivity may contribute to harmful immune responses towards the allograft, provided that the cross-reactive T cells get sufficiently activated upon recognition of the allo-HLA. An important determinant of T-cell activation is TCR avidity, which to date, has remained largely unexplored for allo-HLA-cross-reactive virus-specific T cells.For this purpose, cold target inhibition assays were performed using allo-HLA-cross-reactive virus-specific memory CD8⁺ T-cell clones as responders, and syngeneic cells loaded with viral peptide and allogeneic cells as hot (radioactively-labeled) and cold (non-radioactively-labeled) targets. CD8 dependency of the T-cell responses was assessed using interferon γ (IFNγ) enzyme-linked immunosorbent assay (ELISA) in the presence and absence of CD8-blocking antibodies.At high viral-peptide loading concentrations, T-cell clones consistently demonstrated lower avidity for allogeneic versus viral epitopes, but at suboptimal concentrations the opposite was observed. In line, anti-viral reactivity was CD8 independent at high, but not at suboptimal viral-peptide-loading concentrations.The avidity of allo-HLA-cross-reactive virus-specific memory CD8⁺ T cells is therefore highly dependent on epitope expression, and as a consequence, can be both higher and lower for allogeneic versus viral targets under different (patho)physiological conditions.     

A spatial view of the CD8+ T-cell response: the case of HCV

In viral infections, a memory T-cell population comprises multiple subtypes of cells, distributed in diverse anatomic compartments and possibly re-circulating among them. Accordingly, memory T cells display distinct phenotypes and functions, depending on the nature of the infecting virus, the anatomic location of the infection, and the differences between the sites of active infection and T-cell collection. This paper explores the body compartments where virus-specific CD8(+) T cells have been found during chronic hepatitis C virus infection, describes the cells' memory qualities, and discusses how they are spatially regulated, in comparison with other human viral infections. Understanding the role of compartmentalization and diversity of HCV-specific memory T-cell subsets may be the key to developing effective immunotherapies.     

Simultaneous Analysis of In Vivo CD8+ T Cell Cytotoxicity Against Multiple Epitopes using Multicolor Flow Cytometry

CD8+ T cells play a critical role in host defense against infections and tumors. Analysis of cytotoxic function of antigen-specific CD8+ T cells in animal models would be important in optimizing vaccine design against infections and tumors. In vivo cytotoxicity assays using fluorescent cellular dyes have been used as a popular alternative to traditionally used in vitro ⁵¹Cr-release assays. With the identification of multiple epitopes in various pathogen models, methods to simultaneously analyze cytotoxicity of CD8+ T cells to multiple epitopes in vivo would assist studies which aim to generate protective CD8+ T cell immunity to multiple epitopes. In this study, we evaluate the use of multiple fluorescent cellular dyes for the in vivo cytotoxicity assay. The use of 3 dyes allowed us to analyze the cytotoxicity of antigen-specific CD8+ T cell populations to multiple epitopes generated by virus infections, as well as their functional avidity, in vivo. Our studies extend the use of in vivo cytotoxicity assays to allow direct comparisons of cytotoxicity to various epitopes in the same animal and may also be applicable to assessment of in vitro cytotoxicity of human CD8+ T cells specific for multiple viral or tumor antigens in clinical settings.     

Critical role for IL-21 in both primary and memory anti-viral CD8+ T-cell responses

While it is well established that CD8(+) T cells generated in the absence of CD4(+) T cells mediate defective recall responses, the mechanism by which CD4(+) T cells confer help in the generation of CD8(+) T-cell responses remains poorly understood. To determine whether CD4(+) T-cell-derived IL-21 is an important regulator of CD8(+) T-cell responses in help-dependent and -independent viral infections, we examined these responses in the IL-21Rα(-/-) mouse model. We show that IL-21 has a role in primary CD8(+) T-cell responses and in recall CD8(+) T-cell responses in help-dependent viral infections. This effect is due to a direct action of IL-21 in enhancing the proliferation of virus-specific CD8(+) T cells and reducing their TRAIL expression. These findings indicate that IL-21 is an important mediator of CD4(+) T-cell help to CD8(+) T cells.     

Enhanced cellular immune response and reduced CD8(+) lymphocyte apoptosis in acutely SIV-infected Rhesus macaques after short-term antiretroviral treatment

Losing the decisive virus-specific functions of both CD4(+) and CD8(+) T lymphocytes in the first weeks after immunodeficiency virus infection ultimately leads to AIDS. The SIV/rhesus monkey model for AIDS was used to demonstrate that a 4-week chemotherapeutic reduction of viral load during acute SIV infection of macaques allowed the development of a competent immune response able to control virus replication after discontinuation of treatment in two of five monkeys. Increasing SIV-specific CD4(+) T-helper-cell proliferation was found in all macaques several weeks after treatment, independent of their viral load. However, only macaques with low viral loads showed persistent T-cell reactivity of lymph node cells. In contrast to animals with higher viral loads, T-helper-cell counts and memory T-helper cells did not decline in the two macaques controlling viral replication. Lymphocyte apoptosis was consistently low in all treated macaques. In contrast, high CD8(+) lymphocyte death but only slightly increased CD4(+) lymphocyte apoptosis were observed during the first weeks after infection in untreated control animals, indicating that early apoptotic death of virus-specific CTL could be an important factor for disease development. Antiretroviral treatment early after infection obviously retained virus-specific and competent T lymphocytes, whereby a virus-specific immune response could develop in two animals able to control the viral replication after cessation of treatment.     

Memory CD8+ T Cells Are Sufficient To Alleviate Impaired Host Resistance to Influenza A Virus Infection Caused by Neonatal Oxygen Supplementation

Supplemental oxygen administered to preterm infants is an important clinical intervention, but it is associated with life-long changes in lung development and increased sensitivity to respiratory viral infections. The precise immunological changes caused by neonatal oxygen treatment remain poorly understood. We previously reported that adult mice exposed to supplemental oxygen as neonates display persistent pulmonary inflammation and enhanced mortality after a sublethal influenza A virus infection. These changes suggest that neonatal hyperoxia impairs the cytotoxic CD8(+) T cell response required to clear the virus. In this study, we show that although host resistance to several different strains of influenza A virus is reduced by neonatal hyperoxia, this treatment does not impair viral clearance, nor does it alter the magnitude of the virus-specific CD8(+) T cell response to primary infection. Moreover, memory T cells are sufficient to ameliorate the increased morbidity and mortality and alleviate the excessive lung damage observed in mice exposed to high oxygen levels as neonates, and we attribute this sufficiency principally to virus-specific memory CD8(+) T cells. Thus, we show that neonatal hyperoxia reduces host resistance to influenza virus infection without diminishing the function of cytotoxic T lymphocytes or the generation of virus-specific memory T cells and that CD8(+) memory T cells are sufficient to provide protection from negative consequences of this important life-saving intervention. Our findings suggest that vaccines that generate robust T cell memory may be efficacious at reducing the increased sensitivity to respiratory viral infections in people born prematurely.     

CD4+ T cells control measles virus infection of the central nervous system.

CD4+ T-cell lines with specificity for individual measles virus (MV) structural proteins were obtained from immunized Lewis rats. Isolated viral proteins, either purified from virions or bacterially expressed were used as antigens for immunological assays. All the cell lines secreted interferon-gamma (IFN-gamma) and interleukin-2 (IL-2), but were only weakly cytotoxic to autologous MV-infected astrocytes. When cultured together with memory splenic B lymphocytes these T cells did not induce secretion of MV-specific antibodies. The in vivo function of the T-cell lines was investigated in our MV-encephalitis model in the Lewis rat. Within 24 hr of intracerebral infection, adoptive transfer of single MV protein-specific T cells either decreased or prevented the subsequent clinical and histological disease depending on the MV-protein specificity of the cell lines. Furthermore, there was an earlier and enhanced viral clearance from the CNS, without a change in the anti-MV antibody titres of serum and cerebrospinal fluid (CSF) of the recipients and the control-infected animals. Prior depletion of CD8+ T lymphocytes in the recipient animals did not abrogate the protection conferred by CD4+ T-cell lines, indicating that the acute viral CNS disease is being efficiently controlled by virus-specific CD4+ T cells.     

T-cell help permits memory CD8(+) T-cell inflation during cytomegalovirus latency

CD4(+) T cells are implied to sustain CD8(+) T-cell responses during persistent infections. As CD4(+) T cells are often themselves antiviral effectors, they might shape CD8(+) T-cell responses via help or via controlling antigen load. We used persistent murine CMV (MCMV) infection to dissect the impact of CD4(+) T cells on virus-specific CD8(+) T cells, distinguishing between increased viral load in the absence of CD4(+) T cells and CD4(+) T-cell-mediated helper mechanisms. Absence of T-helper cells was associated with sustained lytic MCMV replication and led to a slow and gradual reduction of the size and function of the MCMV-specific CD8(+) T-cell pool. However, when virus replication was controlled in the absence of CD4(+) T cells, CD8(+) T-cell function was comparably impaired, but in addition CD8(+) T-cell inflation, a hallmark of CMV infection, was completely abolished. Thus, CD8(+) T-cell inflation during latent CMV infection is strongly dependent on CD4(+) T-cell helper functions, which can partially be compensated by ongoing lytic viral replication in the absence of CD4(+) T cells.     

Infection with a virus generates a polyclonal immune response with broad alloreactive potential

Virus-specific T cells have been shown to cross-react with allogeneic HLA (allo-HLA) at a clonal level. However, the impact of a single virus on the allorepertoire has never been investigated at the polyclonal level.We made an inventory of the incidence and specificity of allo-HLA-cross-reactive-virus-specific CD8⁺ T cells in 24 healthy individuals. T cells were stained for 25 virus-specific tetramers, and mixed-lymphocyte reactions were performed against a panel of HLA-typed allostimulators. Allospecificity was confirmed by IFNγ-ELISA using T-cell clones against a panel of HLA-typed cell-lines.The polyclonal immune repertoire directed against CMV alone was associated with a memory response against six allo-HLA molecules. Besides, a single allostimulator activated memory T-cell responses with multiple viral specificities.Concluding, a single virus can substantially broaden the allo-HLA memory T-cell repertoire. This study only looked at CMV- and EBV-specific T cells, whereas the immune repertoire consists of T cells directed against many different viruses. Hence, transplant patients receiving an HLA-mismatched graft may already express a polyclonal repertoire of anti-donor-memory T cells before transplantation.     

Analysis of the T-cell micro-environment in Epstein–Barr virus-related post-transplantation B lymphoproliferative disease

Epstein–Barr virus (EBV) post-transplantation B lymphoproliferative disease (BLPD) may undergo regression after immunosuppression withdrawal and restoration of EBV-specific cytotoxic T-cell (CTL) activity in the immunocompromised allografted host. The presence of morphologically normal T cells in the BLPD micro-environment may influence tumour behaviour in vivo. In this immunopathological study, the phenotype and the number of T cells and other immunoregulatory cells have been investigated in seven primary and four recurrent BLPD biopsies from nine solid organ transplant recipients. BLPD with either viral lymphadenopathic or polymorphic lymphoma appearances was found to contain sizeable T-cell populations, mainly of memory/helper (TCRα/β+, CD3+, CD4+, CD45RO+) type. Cytotoxic (TCRα/β+, CD3, CD8+, Tia-1+) T cells were strikingly low in all samples. Low CD28 and CD25 expression suggested that secondary signals for functional and sustained T-cell activation may be deficient in these tumours. No close correlation was found between the degree of T-cell infiltration and clinical outcome, although appreciably higher numbers of CD8+ T cells were detected in three BLPD tumours showing prolonged clinical remission after treatment. While some level of EBV-specific T-cell function may be present in untreated BLPD, the overall findings of this study suggest that the nature of T-cell infiltrates may reflect a response to immunosuppressive therapy rather than to EBV infection per se. The possibility that a local EBV-specific T-cell response is generated in BLPD undergoing regression after treatment needs to be investigated. © 1998 John Wiley & Sons, Ltd.     

TGF-β blockade does not improve control of an established persistent viral infection

Acute resolving viral infections are often associated with a strong and multi-specific T-cell response, whereas in persistent viral infections T-cell responses are often impaired. It has been suggested that the resuscitation of the antiviral T-cell response could be a powerful tool to target persisting viruses. Several immunoregulatory pathways, such as IL-10 and TGF-β, have been shown to be involved in the induction of T-cell exhaustion and viral persistence. In this study, we sought to investigate whether TGF-β signaling is also relevant in the maintenance of T-cell exhaustion after viral persistence has been established, and whether blockade of TGF-β signaling could improve control of viral replication in a mouse model of persistent virus infection. Using the LCMV clone 13 model, we analyzed the frequency, function, and phenotype of virus-specific CD4 and CD8 T cells following therapeutic TGF-β signaling blockade. We show that in vivo blockade of the TGF-β receptor failed to substantially enhance the antiviral T-cell response, and was insufficient to mediate a therapeutically-relevant reduction of viral titers in different tissues. Thus, although TGF-β signaling has the ability to hamper antiviral immunity, its pharmacological blockade may not be sufficient to tackle persistent viruses.     

Failing immune control as a result of impaired CD8+ T-cell maturation: CD27 might provide a clue

Despite readily detectable virus-specific CD8(+) T cells in most HIV-infected patients, immune surveillance is eventually lost, leading to progression to AIDS. Recently developed insights into human T-cell differentiation have been used to study the phenotype of virus-specific T cells in HIV-infected individuals. Based on these results, we propose that failing immune control in human viral infection could be a result of impaired cytotoxic T-lymphocyte (CTL) maturation into fully differentiated effector T cells. Impaired maturation is not confined to HIV-specific CD8(+) T cells but could also be involved in failing immunity to Epstein-Barr virus and other viral infections. We postulate that CD27(-) effector CD8(+) T cells might be required for adequate control of chronic viral infection and prevention of disease development.     

Estimation of human and animal immunological memory by testing the trogocytosis of virus-specific T lymphocytes

This study is the first attempt to evaluate the immunogenicity of Russian live attenuated influenza reassortant influenza vaccine (LAIV), by using a modified T-cell recognition of antigen presenting cells by protein capture (TRAP) method. Single vaccination of 18-20-year-old volunteers with LAIV causes an increase in the peripheral blood levels of virus-specific memory CD4+ T lymphocytes. Some (40-60%) LAIV-vaccination volunteers respond to immunization by showing a significant elevation in the peripheral blood level of memory CD4+ T cells without a systemic humoral immune response recorded in the passive hemagglutination test. Vaccination of mice with live attenuated A (H1N1) influenza reassortant virus stimulates the production of memory CD8+CD44hi T lymphocytes in the nasal-associated lymphoid tissue, the entry of infection, so does influenza infection. Vaccination with inactivated A (H1N1) influenza virus practically fails to induce these cells. A (H1N1) influenza virus-specific CD8+CD44hi T lymphocytes remain within at least 2 months (observation time). The authors' modified TRAP may be used to evaluate virus-specific immunological T-cell memory after vaccination.     

T cell immunodominance and maintenance of memory regulated by unexpectedly cross-reactive pathogens

We show here that T cell cross-reactivity between heterologous viruses influences the immunodominance of virus-specific CD8(+) T cells by two mechanisms. First, T cells specific for cross-reactive epitopes dominate acute responses to viral infections; second, within the memory pool, T cells specific for cross-reactive epitopes are maintained while those specific for non-cross-reactive epitopes are selectively lost. These findings suggest an immunological paradigm in which viral infections shape the available T cell repertoire, causing alterations in the hierarchies of both the primary and memory CD8(+) T cell responses elicited by subsequent viral infections. Thus, immunodominance is a function of the host's previous exposure to unrelated pathogens, and this may have an impact on protective immunity and immunopathology.     

FURIN regulates cytotoxic T-lymphocyte effector function and memory cell transition in mice

The proprotein convertase subtilisin/kexins (PCSKs) regulate biological actions by cleaving immature substrate proteins. The archetype PCSK, FURIN, promotes the pathogenicity of viruses by proteolytically processing viral proteins. FURIN has also important regulatory functions in both innate and adaptive immune responses but its role in the CD8⁺ CTLs remains enigmatic. We used a T-cell-specific FURIN deletion in vivo to demonstrate that FURIN promotes host response against the CTL-dependent lymphocytic choriomeningitis virus by virtue of restricting viral burden and augmenting interferon gamma (IFNG) production. We also characterized Furin KO CD8⁺ T cells ex vivo, including after their activation with FURIN regulating cytokines IL12 or TGFB1. Furin KO CD8⁺ T cells show an inherently activated phenotype characterized by the upregulation of effector genes and increased frequencies of CD44⁺, TNF⁺, and IFNG⁺ cells. In the activated CTLs, FURIN regulates the productions of IL2, TNF, and GZMB and the genes associated with the TGFBR-signaling pathway. FURIN also controls the expression of Eomes, Foxo1, and Bcl6 and the levels of ITGAE and CD62L, which implies a role in the development of CTL memory. Collectively, our data suggest that the T-cell expressed FURIN is important for host responses in viral infections, CTL homeostasis/activation, and memory development.     

Waking up T cells to counteract chronic infections

Memory T-cell responses generated in chronic viral infections can show functional defects contributing to poor viral control. Recently, signaling through the PD-1 receptor on CD8+ T cells was shown to cause cells to express an exhausted phenotype in an animal model of chronic infection. By blocking the interaction of PD-1 with its ligand PD-L1, virus-specific CD8+ T cells exhibited expansion and improved infection control. This approach could prove valuable to manage chronic infections.