V(D)J recombination is essential for developing lymphocytes and the specific functioning of the immune system. Germline gene coding segments become rearranged to create functional immunoglobulin and T-cell receptor genes by this recombination. The process depends on site-specific cleavage of chromosomal DNA by RAG-1 and RAG-2 recombinase. Two recombination-activating gene proteins (RAG-1/2) in conjunction make up a complex of enzymes that join gene segments of B-cell and T-cell receptor genes. RAG-1 contains most of the V(D)J recombinase active site and RAG-2 is essential in joining DNA segments during V(D)J recombination. RAG-1/2 have similarity in action to other DNA transposases and HIV-1 integrase. These similarities suggest that HIV-1 integrase inhibitors may have the potential to affect aspects of both B-cell and T-cell development.

Induction of primary immune responses to neoantigens involves the generation of specific T-cells and immunoglobulin M (IgM) antibody secreting B-cells. As part of this process, T and B memory cells are also generated, which have specific cell surface receptors to the antigen. On repeat exposure to the antigen, these memory T- and B-cells are triggered to generate rapid and intense secondary responses. During this secondary response, B-cells secrete abundant specific IgG antibodies with greater affinity to the antigen than for the IgM isotope. This memory response is mediated by T-cells with CD45+ RO+ phenotype. These T-cells provide B-cells the help required to generate the specific IgG. Sub-optimal antibody responses are seen in both acquired and hereditary immunodeficiency, which are due to impaired T-cell function including poor T-helper responses to B-cells and defective neo-antigen responses.

An established method to evaluate T-cell function involves testing antibody production to vaccination with phiX174, a stable bacteriophage of E. Coli that is critical in demonstrating T-cell competence. Antibody titers after primary and secondary immunization correlate with abnormal CD4 cell help. Patients with functional B-cells that lack T-cell help show a characteristic failure to switch from IgM to IgG, making this assay essential in the evaluation of V(D)J recombination.

Currently, raltegravir is the only approved integrase inhibitor that targets the integration stage of the HIV-1 lifecycle. The clinical manifestations of raltegravir-related potential adverse effects on V(D)J recombination may be so rare that they may only be observed after large numbers of patients are exposed to this drug. Evaluating the direct in vivo interaction of HIV integrase inhibitors on RAG-1/2 is difficult, therefore the best approach may be to evaluate the potential negative effects on recombinase activity downstream by studying immune function. If gene rearrangements of immunoglobulin and T-cell receptor genes are altered by HIV integrase, then patient lymphocytes will fail to display normal responses to neo-antigen exposure. Since untreated HIV-infected individuals have an impaired ability to respond to new antigens, it is difficult to evaluate the responses to neo-antigens in these individuals. Therefore, to test this hypothesis, it would be best to choose patients with long-term control of HIV that have recovered immune function.