Therapeutic Vaccine Against HIV,Viral Variability,Cytotoxic T Lymphocyte Epitopes,and Genetics of Patients

Introduction

HIV-1 infection is a chronic infection that induces a steady decrease in CD4⁺ T lymphocytes and leads to AIDS. The emergence of tritherapies and diversification of antiretroviral agents have made it possible to control viral replication in treated patients, resulting in the restitution of their immune defenses and allowing them to lead a normal life. However, these treatments are costly and have side effects. Trials in which treatment was discontinued were followed by a resumption of viral replication. ¹ Indeed, after the primary infection phase, HIV-1 establishes a cell reservoir, the CD4⁺ memory T cells, where it becomes latent, ² and anatomical reservoirs such as the central nervous and genital systems, the lymph nodes that are not fully permeable to some antiretroviral molecules, and the gastrointestinal associated lymphoid tissues. Therefore, the virus replication resumes significantly while the patient is experiencing a therapeutic interruption; moreover, it seems that residual replication persists in the reservoir cells during the control phase of viral replication at loads less than the quantification thresholds. ³

The scientific and medical community is now seeking to cure HIV. Several pathways have been or are being explored ⁴ : therapeutic intensification, latency reversal agents such as histone deacetylase that force the provirus to express itself with a resumption of productive viral replication, and exposure to cytotoxic CD8⁺ T lymphocytes (“shock and kill”), monoclonal antibodies, immunomodulators (such as IL7 and PD-1 inhibitor), gene therapy (delivery in infected cells of zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), or clustered regularly interspaced short palindromic repeats (CRISPR) nucleases/Cases9), and therapeutic vaccination. At present, only one patient in the world has been successfully cured of HIV. This is the “Berlin patient” who, during his exceptional clinical and therapeutic history, received a graft of delta 32 CCR5 lymphocytes that could no longer serve as a target for viral replication. ⁵

Therapeutic Vaccination

It was Salk who first and very early in the history of the discovery of AIDS and HIV-1 had the idea to vaccinate HIV-1-positive patients against the virus using inactivated and viral particles depleted in Gp120 (HIV-1 Immunogen Remune). ⁶ This attempt was not successful. Since then, and more recently, other vaccine constructs have been tested, of which this article gives a summary. First, viroimmunological studies on primary infection as well as on long-term nonprogressing patients, called elite controllers, have demonstrated the importance of the CD8⁺ T cell cytotoxic response ⁷ and have mainly oriented research on vaccine constructs toward this type of response, without ignoring antibody-dependent cellular toxicity neutralizing antibodies. A special comment must be made here on the CD4⁺ T cell response; this response is restricted by HLA II alleles and is of help to the synthesis of antibodies by B lymphocytes and to the CD8⁺ T cell response; some vaccine constructions have integrated antigens for both CD4⁺ end CD8⁺ T responses, but due to the general knowledge that CD8⁺ T cells are highly efficient for viral clearance, most of the therapeutic vaccines have focused on stimulation of CD8⁺ rather than CD4⁺ T cell response ^8,9

Table 1 summaries the different vaccine constructions and the main trials in HIV-infected patients on successful combination ART.

Viral/Proviral Variability and Patient Genetics

The results of these trials are clearly not commensurate with the hope placed in them. Might there be one or more uncontrolled variables? It should first be emphasized that most vaccine constructs are based on generic HIV-1 viruses and that circulating strains may exhibit variations, especially regarding the CTL epitopes that must be presentable to antigens linked to HLA I alleles. In infected subjects and owing to a process of drift induced by reverse transcriptase errors and the development of subspecies, the number of mutated CTL epitopes increases with time since the primary infection phase. In contrast, the virus, which multiplies after discontinuation of treatment, originates mainly from the cellular reservoir represented by the CD4⁺ memory T cells, which are reactivated. The virus, therefore, leaves an archived viral DNA that is not strictly identical to the virus that was circulating before the antiretroviral treatment. This means that what has been archived is probably the image of what will be reactivated. In addition, no vaccine construct based on the genetic characteristics of patients has been developed to date. However, whether they are provided by recombinant viruses, plasmid DNA, or directly in the form of lipopeptides, CTL epitopes must be presented by HLA I allele antigens, a process that depends on the genetics of patients. Our team has drawn attention to this discrepancy between the archived epitopes and the theoretical recognition by the HLA alleles, ^19,20 and a very thorough study of a similar nature was published by Siliciano's team. ²¹ They raised the issue of the adequacy between archived CTL epitopes and vaccine CTL epitopes, which are preserved epitopes. They have confirmed that, at interruption of ART, the virus resumes from proviral DNA of CD4+ memory T cells; therefore, they have characterized and compared by high-throughput sequencing the CTL epitopes from the archived virus with those from the virus produced by these cells in culture. The aim of such work is to identify nonvariable epitopes in the provirus that can be used to induce a vaccine response. In contrast, proviral sequence studies are promising, even though the majority of proviral sequences do not generate infectious viruses. ²²

Of course, the genetics of patients need to be taken into consideration, especially their HLA alleles. Indeed, it can be hypothesized that generic CTL epitopes introduced into vaccine constructs will generate an immune response, but only if the presentation allele is present. There is, therefore, a need to find a balance between the conservation of CTL epitopes and presentation by HLA alleles.

This presentation by HLA alleles is being increasingly understood. ²³ Some alleles are associated with a slower evolution of HIV-1 infection such as HLA-B*27 and HLA-B*57. A study of elite controllers confirmed the role of CTL in controlling infection. ²⁴ Recently, it was found that the vaccine used in the RV144 preventive vaccination trial was more effective in HLA-A*02 patients. ²⁵ To add further complexity to the subject, adaptation of the virus to HLA class I alleles has been demonstrated ²⁶ : in that study, the authors showed in >2,800 patients that the frequency of their epitopic variants was correlated with their restriction alleles, raising the hypothesis of an adaptation of the virus to class I HLA alleles in a given population. Similarly, a Japanese study showed how an Nef-Y 135F mutant escapes presentation by the HLA-A*24:02 allele, which is expressed by >60% of the Japanese population. ²⁷

The pathway is, therefore, a narrow one between adaptation of the virus to HLA I restriction and the definition of conserved proviral CTL epitopes presentable by HLA I alleles. A rational strategy would be to sequence the archived provirus of patients in therapeutic success and then to synthesize peptides corresponding to their presentable CTL epitopes, on the basis of their HLA alleles characterized by molecular biology or even by high-throughput sequencing. This would be tantamount to creating a personalized vaccine. However, the industrial issues are complex, if not insurmountable. Another strategy is to identify CTL epitopes preserved on the basis of the frequency of alleles in specific populations, to synthesize peptide assemblies presentable by the most frequent alleles and haplotypes. ²⁸ It is likely that the genetics of patients will need to be considered for HIV-1 vaccine studies and that multidisciplinary collaboration will be essential in this field of infectious diseases.