The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP

Chimeric Antigen Receptors Expand the Repertoire of Antigenic Macromolecules for Cellular Immunity

T-cell therapies have made significant improvements in cancer treatment over the last decade. One cellular therapy utilizing T-cells involves the use of a chimeric MHC-independent antigen-recognition receptor, typically referred to as a chimeric antigen receptor (CAR). CAR molecules, while mostly limited to the recognition of antigens on the surface of tumor cells, can also be utilized to exploit the diverse repertoire of macromolecules targetable by antibodies, which are incorporated into the CAR design. Leaning into this expansion of target macromolecules will enhance the diversity of antigens T-cells can target and may improve the tumor-specificity of CAR T-cell therapy. This review explores the types of macromolecules targetable by T-cells through endogenous and synthetic antigen-specific receptors.

Role of CD8+ T Cells in the Selection of HIV-1 Immune Escape Mutations

Human immunodeficiency virus type-1 (HIV-1) infection represents one of the biggest public health problems worldwide. The immune response, mainly the effector mechanisms mediated by CD8⁺ T cells, induces the selection of mutations that allows the virus to escape the immune control. These mutations are generally selected within CD8⁺ T cell epitopes restricted to human leukocyte antigen class I (HLA-I), leading to a decrease in the presentation and recognition of the epitope, decreasing the activation of CD8⁺ T cells. However, these mutations may also affect cellular processing of the peptide or recognition by the T cell receptor. Escape mutations often carry a negative impact in viral fitness that is partially or totally compensated by the selection of compensatory mutations. The selection of either escape mutations or compensatory mutations may negatively affect the course of the infection. In addition, these mutations are a major barrier for the development of new therapeutic strategies focused on the induction of specific CD8⁺ T cell responses.

HIV competition dynamics over sexual networks: first comer advantage conserves founder effects

Outside Africa, the global phylogeography of HIV is characterized by compartmentalized local epidemics that are typically dominated by a single subtype, which indicates strong founder effects. We hypothesized that the competition of viral strains at the epidemic level may involve an advantage of the resident strain that was the first to colonize a population. Such an effect would slow down the invasion of new strains, and thus also the diversification of the epidemic. We developed a stochastic modelling framework to simulate HIV epidemics over dynamic contact networks. We simulated epidemics in which the second strain was introduced into a population where the first strain had established a steady-state epidemic, and assessed whether, and on what time scale, the second strain was able to spread in the population. Simulations were parameterized based on empirical data; we tested scenarios with varying levels of overall prevalence. The spread of the second strain occurred on a much slower time scale compared with the initial expansion of the first strain. With strains of equal transmission efficiency, the second strain was unable to invade on a time scale relevant for the history of the HIV pandemic. To become dominant over a time scale of decades, the second strain needed considerable (>25%) advantage in transmission efficiency over the resident strain. The inhibition effect was weaker if the second strain was introduced while the first strain was still in its growth phase. We also tested how possible mechanisms of interference (inhibition of superinfection, depletion of highly connected hubs in the network, one-time acute peak of infectiousness) contribute to the inhibition effect. Our simulations confirmed a strong first comer advantage in the competition dynamics of HIV at the population level, which may explain the global phylogeography of the virus and may influence the future evolution of the pandemic.

The African epicentre of the HIV pandemic is home to a vast array of divergent viruses; however, local epidemics in other parts of the world are typically dominated by a single variant (subtype) of the virus, with different subtypes found in the different regions. This pattern indicates that local epidemics outside Africa have been started by the introduction of single “founder” viruses in the susceptible populations. However, how these patterns persisted over several decades in the face of international migration requires further explanation. By analyzing simulated epidemics, we demonstrated that an epidemic established by the first successful founder strain can inhibit the introduction and slow down the subsequent spread of further virus strains by several mechanisms of interference. Our results have implications for the global evolution of the HIV pandemic: the fast expansion of subtypes benefited from a “first comer advantage,” and founder viruses may have been selected by random sampling, rather than due to superior transmissibility/fitness; the fast expansion of these (possibly) suboptimal virus strains may have considerably delayed the spread of more transmissible HIV variants; however, the future evolution of the pandemic is likely to be characterized by a slow expansion of viral strains with increased transmission potential.

Differential characteristics of cytotoxic T lymphocytes restricted by the protective HLA alleles B*27 and B*57 in HIV-1 infection

OBJECTIVE

HLA-B*27 and B*57 are associated with relatively slow progression to AIDS. Mechanisms held responsible for this protective effect include the immunodominance and high magnitude, breadth, and affinity of the cytotoxic T lymphocytes (CTL) response restricted by these HLA molecules, as well as superior maintenance of CTL responses during HIV-1 disease progression.

DESIGN

We examined CTL responses from HIV-1-infected individuals restricted through protective and nonprotective HLA alleles within the same host, thereby excluding any effects of slow or rapid progression on the CTL response.

RESULTS

We found that neither immunodominance, nor high magnitude and breadth, nor affinity of the CTL response are general mechanisms of protection against disease progression. HLA-B*57-restricted CTL responses were of exceptionally high affinity and dominated the HLA-A*02-restricted CTL response in individuals coexpressing these HLA alleles. In contrast, HLA-B*27-restricted CTL responses were not of particularly high affinity and did not dominate the response in individuals coexpressing HLA-B*27 and HLA-A*02. Instead, in individuals expressing HLA-B*27, the CTL response restricted by nonprotective HLA alleles was significantly higher and broader, and of higher affinity than in individuals expressing these alleles without HLA-B*27. Although HLA-B*27 and B*57 are thought to target the most conserved parts of HIV, during disease progression, CTL responses restricted by HLA-B*27 and B*57 were lost at least as fast as CTL responses restricted by HLA-A*02.

CONCLUSIONS

Our data show that many of the mechanisms of CTL that are generally held responsible for slowing down HIV-1 disease progression hold for HLA-B*57 but do not hold for HLA-B*27.

Viral CD8 T cell epitope nucleotide composition shows evidence of short- and long-term evolutionary strategies

Viral epitopes have a distinct codon usage that reflects their dual role in infection and immunity. On the one hand, epitopes are part of proteins important to viral function; on the other hand, they are targets of the immune response. Studies of selection are most commonly based on changes of amino acid and seen through the accumulation of non-synonymous mutations. An independent measure of selection is the codon usage and underlying changeability of the nucleotide sequences. We here use multiple tools and a large-scale analysis of viral genomes to demonstrate that viral epitopes have a distinct codon usage and that this codon usage reflects distinct short- and long-term types of selection during viral evolution. We show that CD8(+) T cell epitopes are encoded by codons more distant from stop codons and more changeable than codons outside epitopes. This biased codon usage reflects the viral population toggling back and forth from a wild-type sequence to an escape mode, which enable them to avoid immune detection when needed, and go back to the functionally favorable form when the threat is removed (i.e., in a new host).

Immune activation promotes evolutionary conservation of T-cell epitopes in HIV-1

HIV, unlike other viruses, may benefit from immune recognition by preserving the sequence of its T cell epitopes, thereby enhancing transmission between cells.

The immune system should constitute a strong selective pressure promoting viral genetic diversity and evolution. However, HIV shows lower sequence variability at T-cell epitopes than elsewhere in the genome, in contrast with other human RNA viruses. Here, we propose that epitope conservation is a consequence of the particular interactions established between HIV and the immune system. On one hand, epitope recognition triggers an anti-HIV response mediated by cytotoxic T-lymphocytes (CTLs), but on the other hand, activation of CD4⁺ helper T lymphocytes (T_H cells) promotes HIV replication. Mathematical modeling of these opposite selective forces revealed that selection at the intrapatient level can promote either T-cell epitope conservation or escape. We predict greater conservation for epitopes contributing significantly to total immune activation levels (immunodominance), and when T_H cell infection is concomitant to epitope recognition (trans-infection). We suggest that HIV-driven immune activation in the lymph nodes during the chronic stage of the disease may offer a favorable scenario for epitope conservation. Our results also support the view that some pathogens draw benefits from the immune response and suggest that vaccination strategies based on conserved T_H epitopes may be counterproductive.

A key component of the immune response against viruses and other pathogens is the recognition of short foreign protein sequences called epitopes. However, viruses can escape the immune system by mutating, so epitopes should accumulate high levels of genetic variability. This has been documented in several human viruses, but in HIV, unexpectedly, epitopes tend to be relatively conserved. Here, we propose that this is a consequence of the peculiar interactions that occur between HIV and the immune system. As with other viruses, recognition of HIV epitopes promotes the activation of cytotoxic and helper T lymphocytes, which then orchestrate a cellular immune response. However, HIV infects helper T lymphocytes as their target cell in the body and does so more efficiently when these cells have been activated to participate in an immune response. Mathematical modeling showed that, in some cases, HIV may take advantage of immune activation, thus favoring epitope conservation. This should be more likely to occur with epitopes that trigger more vigorous T-cell responses, and during the process known as “trans-infection,” in which helper T lymphocytes are infected while being activated. Our results highlight the potential advantages of an HIV vaccination strategy based on epitopes that stimulate cytotoxic T lymphocytes without specifically stimulating helper T lymphocytes.

Autologous HIV-1 clade-B Nef peptides elicit increased frequency, breadth and function of CD8+ T-cells compared to consensus peptides

OBJECTIVE

To determine the function and phenotype of CD8(+) T-cells targeting consensus and autologous sequences of entire HIV-1 Nef protein.

METHODS

Multiparameter flow cytometry-based analysis was used to evaluate the responses of two treatment naïve HIV-infected individuals, during primary and the chronic phases of infection.

RESULTS

A greater breadth and magnitude of CD8 IFN-γ responses to autologous compared to clade-B consensus peptides was observed in both subjects. Cross recognition between autologous and consensus peptides decreased in both subjects during progression from primary to chronic infection. The frequencies of TEMRA and TEM CD8(+) T-cells targeting autologous peptides were higher than those targeting consensus peptides and were more polyfunctional (IFN-γ(+) Gr-B(+) CD107a(+)).

CONCLUSIONS

Our data indicate superior sensitivity and specificity of autologous peptides. The functional and maturational aspects of "real" versus "cross-recognized" responses were also found to differ, highlighting the importance of a sequence-specific approach towards understanding HIV immune response.

Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy?

Prediction methods as well as experimental methods for T-cell epitope discovery have developed significantly in recent years. High-throughput experimental methods have made it possible to perform full-length protein scans for epitopes restricted to a limited number of MHC alleles. The high costs and limitations regarding the number of proteins and MHC alleles that are feasibly handled by such experimental methods have made in silico prediction models of high interest. MHC binding prediction methods are today of a very high quality and can predict MHC binding peptides with high accuracy. This is possible for a large range of MHC alleles and relevant length of binding peptides. The predictions can easily be performed for complete proteomes of any size. Prediction methods are still, however, dependent on good experimental methods for validation, and should merely be used as a guide for rational epitope discovery. We expect prediction methods as well as experimental validation methods to continue to develop and that we will soon see clinical trials of products whose development has been guided by prediction methods.

The efficiency of the human CD8+ T cell response: how should we quantify it, what determines it, and does it matter?

Multidisciplinary techniques, in particular the combination of theoretical and experimental immunology, can address questions about human immunity that cannot be answered by other means. From the turnover of virus-infected cells in vivo, to rates of thymic production and HLA class I epitope prediction, theoretical techniques provide a unique insight to supplement experimental approaches. Here we present our opinion, with examples, of some of the ways in which mathematics has contributed in our field of interest: the efficiency of the human CD8+ T cell response to persistent viruses.

Loss of HIV-1-derived cytotoxic T lymphocyte epitopes restricted by protective HLA-B alleles during the HIV-1 epidemic

OBJECTIVE AND DESIGN

HIV-1 is known to adapt to the human immune system, leading to accumulation of escape mutations during the course of infection within an individual. Cross-sectional studies have shown an inverse correlation between the prevalence of human leukocyte antigen (HLA) alleles in a population and the number of cytotoxic T lymphocyte (CTL) escape mutations in epitopes restricted by those HLA alleles. Recently, it was demonstrated that at a population level HIV-1 is adapting to the humoral immune response, which is reflected in an increase in resistance to neutralizing antibodies over time. Here we investigated whether adaptations to cellular immunity have also accumulated during the epidemic.

METHODS

We compared the number of CTL epitopes in HIV-1 strains isolated from individuals who seroconverted at the beginning of the HIV-1 epidemic and from individuals who seroconverted in recent calendar time.

RESULTS

The number of CTL epitopes in HIV-1 variants restricted by the most common HLA alleles in the population did not change significantly during the epidemic. In contrast, we found a significant loss of CTL epitopes restricted by HLA-B alleles associated with a low relative hazard of HIV-1 disease progression during the epidemic. Such a loss was not observed for CTL epitopes restricted by HLA-A alleles.

CONCLUSION

Despite the large degree of HLA polymorphism, HIV-1 has accumulated adaptations to CTL responses within 20 years of the epidemic. The fact that such adaptations are driven by the HLA-B molecules that provide best protection against HIV-1 disease progression has important implications for our understanding of HIV evolution.

Association of TAP 1 and 2 gene polymorphisms with human immunodeficiency virus-tuberculosis co-infection

Major histocompatibility complex (MHC) class I binding peptides are carried from cytosol to the lumen of the endoplasmic reticulum (ER) by transporter associated with antigen processing (TAP), an integral ER membrane protein composed of two subunits, TAP1 and TAP2. Polymorphism in TAP genes may influence these proteins further affecting the antigen peptide presentation, indirectly resulting in the viral escape mechanism from cell-mediated immunity in human immunodeficiency virus (HIV). Our aim was to study the influence of these polymorphism in study groups with HIV-tuberculosis (TB) (n = 110), TB (n = 105), and HIV (n = 130) compared with healthy controls (n = 183), using the tetraprimer amplification refractory mutation system (ARMS)-polymerase chain reaction method. Our results demonstrated that the GG genotype at TAP1 position 333 and GA genotype at TAP1 position 637 were positively associated with HIV-TB co-infection and these genotypes may act as a risk factor for developing TB co-infection in HIV-positive individuals.

HLA class I binding of HBZ determines outcome in HTLV-1 infection

CD8(+) T cells can exert both protective and harmful effects on the virus-infected host. However, there is no systematic method to identify the attributes of a protective CD8(+) T cell response. Here, we combine theory and experiment to identify and quantify the contribution of all HLA class I alleles to host protection against infection with a given pathogen. In 432 HTLV-1-infected individuals we show that individuals with HLA class I alleles that strongly bind the HTLV-1 protein HBZ had a lower proviral load and were more likely to be asymptomatic. We also show that in general, across all HTLV-1 proteins, CD8(+) T cell effectiveness is strongly determined by protein specificity and produce a ranked list of the proteins targeted by the most effective CD8(+) T cell response through to the least effective CD8(+) T cell response. We conclude that CD8(+) T cells play an important role in the control of HTLV-1 and that CD8(+) cells specific to HBZ, not the immunodominant protein Tax, are the most effective. We suggest that HBZ plays a central role in HTLV-1 persistence. This approach is applicable to all pathogens, even where data are sparse, to identify simultaneously the HLA Class I alleles and the epitopes responsible for a protective CD8(+) T cell response.

Quantifying how MHC polymorphism prevents pathogens from adapting to the antigen presentation pathway

The classical antigen presentation pathway consists of two monomorphic (proteasome and TAP) and one polymorphic components (MHC Class I). Viruses can escape CTL responses by mutating an epitope so that it is no longer correctly processed by the pathway. Whereas escape mutations that affect MHC binding are typically no longer under selection pressure in the next host of the virus (as hosts differ in their MHC alleles), escape mutations that affect the antigen processing of epitope precursors prevent the use of those epitope precursors by any of the MHC alleles in a host population. Viruses might therefore be under selection pressure to adapt to the monomorphic proteasome and TAP. We designed an agent-based model of a host population, in which an HIV-1 like virus adapts to the antigen presentation pathway of individual hosts, as the virus spreads through the population. We studied how the polymorphism of the MHC and the monomorphism of the proteasome and TAP affected the level of adaptation to the host population that the virus could reach. We found that due to the polymorphism and high specificity of the MHC class I molecules, the CTL epitopes that are targeted by the CTL responses of different hosts do not share many epitope precursors. Therefore, escape mutations in epitope precursors are frequently released from immune selection pressure, and can revert back to the virus wildtype sequence. As a result, the selection pressure on the virus to adapt to the proteasome and TAP is relatively small, which explains the low level of adaptation of the virus to the monomorphic steps in the antigen presentation pathway.

The distribution of CTL epitopes in HIV-1 appears to be random, and similar to that of other proteomes

Background

HIV-1 viruses are highly capable of mutating their proteins to escape the presentation of CTL epitopes in their current host. Upon transmission to another host, some escape mutations revert, but other remain stable in the virus sequence for at least several years. Depending on the rate of accumulation and reversion of escape mutations, HIV-1 could reach a high level of adaptation to the human population. Yusim et. al. hypothesized that the apparent clustering of CTL epitopes in the conserved regions of HIV-1 proteins could be an evolutionary signature left by large-scale adaptation of HIV-1 to its human/simian host.

Results

In this paper we quantified the distribution of CTL epitopes in HIV-1 and found that that in 99% of the HIV-1 protein sequences, the epitope distribution was indistinguishable from random. Similar percentages were found for HCV, Influenza and for three eukaryote proteomes (Human, Drosophila, Yeast).

Conclusion

We conclude that CTL epitopes in HIV-1 are randomly distributed, and that this distribution is similar to the distribution of CTL epitopes in proteins from other proteomes. Therefore, the visually apparent clustering of CTL epitopes in epitope maps should not be interpreted as a signature of a past large-scale adaptation of HIV-1 to the human cellular immune response.

The HIV hide and seek game: an immunogenomic analysis of the HIV epitope repertoire

BACKGROUND

Viruses employ various means to evade immune detection. One common evasion strategy is the removal of CD8 cytotoxic T-lymphocyte (CTL) epitopes.

METHOD

Here, we use bioinformatic tools to compute the HIV CTL epitope repertoire presented by over 8000 HIV sequences in multiple Human Leukocyte Antigen alleles. We define the 'Size of Immune Repertoire' (SIR) score, which represents the ratio between the number of the predicted epitopes within a protein and their expected number within a scrambled version of the same protein.

RESULTS

We show that HIV proteins present less epitopes than expected and that the number of epitopes gradually decreases from SIV to recent HIV sequences. The decrease of the SIR score of HIV is accompanied by a high frequency of replacement mutations within epitopes. The SIR score of the different HIV proteins is not uniform. The regulatory proteins, Tat and Rev, expressed early during cellular infection have a low SIR score, whereas virion-associated genes that are expressed later, such as Env, Pol and Gag, have a higher SIR score. Actually, the SIR score of Gag keeps increasing over time.

CONCLUSION

We hypothesize that our results reflect an HIV immune evasion strategy. This involves the targeting of the CTL immune response to viral structural and enzyme proteins, allowing the virus a time interval to propagate before its host cells are destroyed by CTLs. An efficient anti-HIV CTL response against HIV should thus also target the regulatory genes that HIV seeks to hide from the immune system.