Alterations in HIV-specific T cell function during acute and early infection

Project Overview

Virus-specific CD8 T cell responses are induced during the acute phase of HIV-1 infection and play an important role in containment of acute viraemia and subsequent control of ongoing viral replication. Prophylactic and therapeutic strategies to combat HIV infection are therefore being designed to target this arm of the immune response. However, moderate-high levels of HIV replication are maintained in the majority of infected individuals despite the presence of high frequencies of HIV-specific CD8 T cells. Mechanisms that impair CD8 T cell control of HIV replication include HIV’s ability to evade CD8 T cell recognition via mutational escape and other strategies such as down-regulation of MHC class I expression on the surface of HIV-infected cells. Importantly, there is also a decline in the antiviral capacity of HIV-specific CD8 T cells during infection. In acute infection HIV-specific CD8 T cells co-express high levels of perforin and granzymes and mediate potent antiviral activity, as evidenced by the rapid kinetics with which they drive selection for T cell escape mutations in the HIV quasispecies. However in the face of continued viral replication they undergo a decline in antiviral effector activity, which is attributed to “exhaustion” driven by constant antigenic stimulation. A more thorough understanding of the alterations that occur in HIV-specific CD8 T cell populations during acute and early infection (including both impairment of antiviral functions and whether other, immunoregulatory functions are acquired)  and the mechanisms that underlie these changes is of importance to enable the development of approaches for preservation and restoration of optimally-effective HIV-specific T cell responses.

In this project, the phenotype and functional capacity of total and HIV-specific CD8 T cells (identified by staining with tetrameric peptide-MHC complexes) will be monitored longitudinally in patients recruited during acute infection and sampled at sequential timepoints during infection. A combination of flow cytometry readouts, gene expression profiling, and in vitro functional assays will be employed to determine the kinetics with which different effector functions of epitope-specific T cell populations alter after acute infection. Expression of costimulatory molecules, inhibitory receptors, cytokine receptors and transcriptional regulators will also be analyzed to gain insight into the mechanisms regulating T cell effector functions. Responses that are rapidly escaped vs not escaped and responses expanded at different times following infection will be studied to determine the impact of ongoing antigenic stimulation and induction of alterations in the immunological environment in inducing the decline in T cell functional capacity. CD4 T cell responses will also be studied in parallel, to give insight into the contribution of antiviral effector CD4 T cells to HIV control and longitudinal alterations in the phenotype and functional capacity of effector CD4 T cell populations.

This ex vivo analysis will also be complemented by in vitro studies to dissect pathways involved in the regulation of T cell functional activity in more depth, e.g. the role of inhibitory receptors that are predominantly expressed on NK cells but can also be expressed on T cells such as KIRs, NKG2A and CD85j, in modulating T cell responsiveness and exhaustion, will be addressed.

Training Opportunities

This project will employ a combination of cellular and molecular immunological techniques, including methods for the isolation of lymphocyte subsets, multiparameter flow cytometry, a broad range of immunoassays and RNASeq-based gene expression analysis. Expertise will also be acquired in HIV growth and titration and viral inhibition assays.  

More generic research training, e.g. in experimental design, data interpretation, statistical analysis and presentation and writing skills will also be provided.

The student will take part in group meetings and journal clubs and will be encouraged to attend seminars given by internal and external speakers. They will also have the opportunity to attend and present their data and national and international meetings.


Immunology & Infectious Disease


Project reference number: 858

Funding and admissions information


Name Department Institution Country Email
Professor Persephone Borrow NDM Research Building Oxford University, NDM Research Building GBR
Dr Dimitra Peppa University College London GBR
Prof Tao Dong Investigative Medicine Division Oxford University, Weatherall Institute of Molecular Medicine GBR

McMichael AJ, Borrow P, Tomaras GD, Goonetilleke N, Haynes BF. 2010. The immune response during acute HIV-1 infection: clues for vaccine development. Nat. Rev. Immunol., 10 (1), pp. 11-23. Read abstract | Read more

The early immune response to HIV-1 infection is likely to be an important factor in determining the clinical course of disease. Recent data indicate that the HIV-1 quasispecies that arise following a mucosal infection are usually derived from a single transmitted virus. Moreover, the finding that the first effective immune responses drive the selection of virus escape mutations provides insight into the earliest immune responses against the transmitted virus and their contributions to the control of acute viraemia. Strong innate and adaptive immune responses occur subsequently but they are too late to eliminate the infection. In this Review, we discuss recent studies on the kinetics and quality of early immune responses to HIV-1 and their implications for developing a successful preventive HIV-1 vaccine. Hide abstract

Ribeiro-dos-Santos P, Turnbull EL, Monteiro M, Legrand A, Conrod K, Baalwa J, Pellegrino P, Shaw GM, Williams I, Borrow P, Rocha B. 2012. Chronic HIV infection affects the expression of the 2 transcription factors required for CD8 T-cell differentiation into cytolytic effectors. Blood, 119 (21), pp. 4928-38. Read abstract | Read more

CD8 T cells lose the capacity to control HIV infection, but the extent of the impairment of CD8 T-cell functions and the mechanisms that underlie it remain controversial. Here we report an extensive ex vivo analysis of HIV-specific CD8 T cells, covering the expression of 16 different molecules involved in CD8 function or differentiation. This approach gave remarkably homogeneous readouts in different donors and showed that CD8 dysfunction in chronic HIV infection was much more severe than described previously: some Ifng transcription was observed, but most cells lost the expression of all cytolytic molecules and Eomesodermin and T-bet by chronic infection. These results reveal a cellular mechanism explaining the dysfunction of CD8 T cells during chronic HIV infection, as CD8 T cells are known to maintain some functionality when either of these transcription factors is present, but to lose all cytotoxic activity when both are not expressed. Surprisingly, they also show that chronic HIV and lymphocytic choriomeningitis virus infections have a very different impact on fundamental T-cell functions, "exhausted" lymphocytic choriomeningitis virus-specific cells losing the capacity to secrete IFN-γ but maintaining some cytotoxic activity as granzyme B and FasL are overexpressed and, while down-regulating T-bet, up-regulating Eomesodermin expression. Hide abstract

Trautmann L, Mbitikon-Kobo FM, Goulet JP, Peretz Y, Shi Y, Van Grevenynghe J, Procopio FA, Boulassel MR, Routy JP, Chomont N, Haddad EK, Sekaly RP. 2012. Profound metabolic, functional, and cytolytic differences characterize HIV-specific CD8 T cells in primary and chronic HIV infection. Blood, 120 (17), pp. 3466-77. Read abstract | Read more

Immediate-early host-virus interactions that occur during the first weeks after HIV infection have a major impact on disease progression. The mechanisms underlying the failure of HIV-specific CD8 T-cell response to persist and control viral replication early in infection are yet to be characterized. In this study, we performed a thorough phenotypic, gene expression and functional analysis to compare HIV-specific CD8 T cells in acutely and chronically infected subjects. We showed that HIV-specific CD8 T cells in primary infection can be distinguished by their metabolic state, rate of proliferation, and susceptibility to apoptosis. HIV-specific CD8 T cells in acute/early HIV infection secreted less IFN-γ but were more cytotoxic than their counterparts in chronic infection. Importantly, we showed that the levels of IL-7R expression and the capacity of HIV-specific CD8 T cells to secrete IL-2 on antigenic restimulation during primary infection were inversely correlated with the viral set-point. Altogether, these data suggest an altered metabolic state of HIV-specific CD8 T cells in primary infection resulting from hyperproliferation and stress induced signals, demonstrate the discordant function of HIV-specific CD8 T cells during early/acute infection, and highlight the importance of T-cell maintenance for viral control. Hide abstract

Demers KR, Makedonas G, Buggert M, Eller MA, Ratcliffe SJ, Goonetilleke N, Li CK, Eller LA, Rono K, Maganga L, Nitayaphan S, Kibuuka H, Routy JP, Slifka MK, Haynes BF, McMichael AJ, Bernard NF, Robb ML, Betts MR. 2016. Temporal Dynamics of CD8+ T Cell Effector Responses during Primary HIV Infection. PLoS Pathog., 12 (8), pp. e1005805. Read abstract | Read more

The loss of HIV-specific CD8+ T cell cytolytic function is a primary factor underlying progressive HIV infection, but whether HIV-specific CD8+ T cells initially possess cytolytic effector capacity, and when and why this may be lost during infection, is unclear. Here, we assessed CD8+ T cell functional evolution from primary to chronic HIV infection. We observed a profound expansion of perforin+ CD8+ T cells immediately following HIV infection that quickly waned after acute viremia resolution. Selective expression of the effector-associated transcription factors T-bet and eomesodermin in cytokine-producing HIV-specific CD8+ T cells differentiated HIV-specific from bulk memory CD8+ T cell effector expansion. As infection progressed expression of perforin was maintained in HIV-specific CD8+ T cells with high levels of T-bet, but not necessarily in the population of T-betLo HIV-specific CD8+ T cells that expand as infection progresses. Together, these data demonstrate that while HIV-specific CD8+ T cells in acute HIV infection initially possess cytolytic potential, progressive transcriptional dysregulation leads to the reduced CD8+ T cell perforin expression characteristic of chronic HIV infection. Hide abstract