Prof Sir Andrew J McMichael

Research Area: Immunology
Scientific Themes: Immunology & Infectious Disease
Keywords: HIV, Vaccines, T cell immunity and Influenza
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Our HIV vaccines have completed five small phase I clinical trials and one large phase I/II clinical trials in London and Oxford. The vaccine is DNA encoding HIV clade A gag p24 and p17 plus a string of epitopes, and the same inserted into recombinant Modified Vaccinia Virus Ankara (MVA). Both stimulate strong CD8+ T cell responses in mice and macaques. In humans both have stimulated measurable CD8+ T cell responses in HIV low risk, uninfected volunteers. Current work is focussing on improving immunogenicity and working out assays for measuring immune responses that are likely to be protective against HIV infection. We tested the effect of those vaccines on boosting T cell responses in HIV infected patients who are on anti-retroviral drugs, with the aim of interrupting drug treatment when the T cell response is enhanced. Encouraging boosts are seen using the MVA-HIVA vaccine.
Nef (key virus protein in virus pathogenesis) initiates a programme of transcription closely similar to that triggered by T cell receptor activation. This favours HIV virus replication. Nef also alters the composition of proteins in cell signalling site, and exclusion of certain regulators favours the activation state.
We continue to explore selection of HIV-1 mutants by the immune response. T cells are very sensitive to small changes in the composition, orientation or flexibility of the exposed peptide bound to HLA. We are studying the immunodominant SLYNTVATL epitope presented by HLA-A2, showing selection of a sequence of mutations that impair T cell recognition. Why the T cells do not respond by new primary responses to the variants is also under investigation.

Name Department Institution Country
Prof Bart Haynes Duke University, North Carolina United States

Ritchie AJ, Cai F, Smith NM, Chen S, Song H, Brackenridge S, Abdool Karim SS, Korber BT, McMichael AJ, Gao F, Goonetilleke N. 2014. Recombination-mediated escape from primary CD8+ T cells in acute HIV-1 infection. Retrovirology, 11 (1), pp. 69. Read abstract | Read more

BACKGROUND: A major immune evasion mechanism of HIV-1 is the accumulation of non-synonymous mutations in and around T cell epitopes, resulting in loss of T cell recognition and virus escape. RESULTS: Here we analyze primary CD8+ T cell responses and virus escape in a HLA B*81 expressing subject who was infected with two T/F viruses from a single donor. In addition to classic escape through non-synonymous mutation/s, we also observed rapid selection of multiple recombinant viruses that conferred escape from T cells specific for two epitopes in Nef. CONCLUSIONS: Our study shows that recombination between multiple T/F viruses provide greater options for acute escape from CD8+ T cell responses than seen in cases of single T/F virus infection. This process may contribute to the rapid disease progression in patients infected by multiple T/F viruses. Hide abstract

Liu MK, Hawkins N, Ritchie AJ, Ganusov VV, Whale V, Brackenridge S, Li H, Pavlicek JW et al. 2013. Vertical T cell immunodominance and epitope entropy determine HIV-1 escape. J Clin Invest, 123 (1), pp. 380-393. Read abstract | Read more

HIV-1 accumulates mutations in and around reactive epitopes to escape recognition and killing by CD8+ T cells. Measurements of HIV-1 time to escape should therefore provide information on which parameters are most important for T cell-mediated in vivo control of HIV-1. Primary HIV-1-specific T cell responses were fully mapped in 17 individuals, and the time to virus escape, which ranged from days to years, was measured for each epitope. While higher magnitude of an individual T cell response was associated with more rapid escape, the most significant T cell measure was its relative immunodominance measured in acute infection. This identified subject-level or "vertical" immunodominance as the primary determinant of in vivo CD8+ T cell pressure in HIV-1 infection. Conversely, escape was slowed significantly by lower population variability, or entropy, of the epitope targeted. Immunodominance and epitope entropy combined to explain half of all the variability in time to escape. These data explain how CD8+ T cells can exert significant and sustained HIV-1 pressure even when escape is very slow and that within an individual, the impacts of other T cell factors on HIV-1 escape should be considered in the context of immunodominance. Hide abstract

Rajapaksa US, Li D, Peng YC, McMichael AJ, Dong T, Xu XN. 2012. HLA-B may be more protective against HIV-1 than HLA-A because it resists negative regulatory factor (Nef) mediated down-regulation. Proc Natl Acad Sci U S A, 109 (33), pp. 13353-13358. Read abstract | Read more

Human leukocyte antigen HLA-B alleles have better protective activity against HIV-1 than HLA-A alleles, possibly due to differences in HLA-restricted HIV-1-specific CD8+ cytotoxic T lymphocyte (CTL) function, but the mechanism is unknown. HIV-1 negative regulatory factor (Nef) mediates down-regulation of surface expression of class I HLA (HLA-I) and may therefore impair immune recognition by CTL. Because of sequence differences in the cytoplasmic domains, HLA-A and -B are down-regulated by Nef but HLA-C and -E are not affected. However, the latter are expressed at low levels and are not of major importance in the CTL responses to HIV-1. Here, we compared the role of the cytoplasmic domains of HLA-A and -B in Nef-mediated escape from CTL. We found HLA-B cytoplasmic domains were more resistant to Nef-mediated down-regulation than HLA-A cytoplasmic domains and demonstrated that these differences affect CTL recognition of virus-infected cells in vitro. We propose that the relative resistance to Nef-mediated down-regulation by the cytoplasmic domains of HLA-B compared with HLA-A contributes to the better control of HIV-1 infection associated with HLA-B-restricted CTLs. Hide abstract

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

Goonetilleke N, Liu MK, Salazar-Gonzalez JF, Ferrari G, Giorgi E, Ganusov VV, Keele BF, Learn GH et al. 2009. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J Exp Med, 206 (6), pp. 1253-1272. Read abstract | Read more

Identification of the transmitted/founder virus makes possible, for the first time, a genome-wide analysis of host immune responses against the infecting HIV-1 proteome. A complete dissection was made of the primary HIV-1-specific T cell response induced in three acutely infected patients. Cellular assays, together with new algorithms which identify sites of positive selection in the virus genome, showed that primary HIV-1-specific T cells rapidly select escape mutations concurrent with falling virus load in acute infection. Kinetic analysis and mathematical modeling of virus immune escape showed that the contribution of CD8 T cell-mediated killing of productively infected cells was earlier and much greater than previously recognized and that it contributed to the initial decline of plasma virus in acute infection. After virus escape, these first T cell responses often rapidly waned, leaving or being succeeded by T cell responses to epitopes which escaped more slowly or were invariant. These latter responses are likely to be important in maintaining the already established virus set point. In addition to mutations selected by T cells, there were other selected regions that accrued mutations more gradually but were not associated with a T cell response. These included clusters of mutations in envelope that were targeted by NAbs, a few isolated sites that reverted to the consensus sequence, and bystander mutations in linkage with T cell-driven escape. Hide abstract

Simmons A, Gangadharan B, Hodges A, Sharrocks K, Prabhakar S, García A, Dwek R, Zitzmann N, McMichael A. 2005. Nef-mediated lipid raft exclusion of UbcH7 inhibits Cbl activity in T cells to positively regulate signaling. Immunity, 23 (6), pp. 621-634. Read abstract | Read more

Lentiviral Nef increases T cell signaling activity, but the molecular nature of the stimulus involved is incompletely described. We explored CD4 T cell lipid raft composition in the presence and absence of Nef. Here, the E2 ubiquitin-conjugating enzyme UbcH7, which acts in conjunction with c-Cbl, is absent from lipid rafts. This Nef-mediated exclusion is associated with failure of ubiquitination of activated Vav. In the presence of Nef, lipid raft Cdc42 is activated and forms a ternary complex between the c-Cbl-interacting protein p85Cool-1/betaPix and c-Cbl, displacing UbcH7 from rafts. Suppression of p85Cool-1/betaPix expression restores UbcH7 raft localization and Vav ubiquitination and diminishes Cdc42 activity. Moreover, p85Cool-1/betaPix knockdown attenuates HIV replication. Thresholds for activation of signaling involve the intricate balance of positive and negative regulators. Here we provide evidence for Nef disruption of a negative regulator of T cell signaling in promoting HIV replication. Hide abstract

Lee JK, Stewart-Jones G, Dong T, Harlos K, Di Gleria K, Dorrell L, Douek DC, van der Merwe PA, Jones EY, McMichael AJ. 2004. T cell cross-reactivity and conformational changes during TCR engagement. J Exp Med, 200 (11), pp. 1455-1466. Read abstract | Read more

All thymically selected T cells are inherently cross-reactive, yet many data indicate a fine specificity in antigen recognition, which enables virus escape from immune control by mutation in infections such as the human immunodeficiency virus (HIV). To address this paradox, we analyzed the fine specificity of T cells recognizing a human histocompatibility leukocyte antigen (HLA)-A2-restricted, strongly immunodominant, HIV gag epitope (SLFNTVATL). The majority of 171 variant peptides tested bound HLA-A2, but only one third were recognized. Surprisingly, one recognized variant (SLYNTVATL) showed marked differences in structure when bound to HLA-A2. T cell receptor (TCR) recognition of variants of these two peptides implied that they adopted the same conformation in the TCR-peptide-major histocompatibility complex (MHC) complex. However, the on-rate kinetics of TCR binding were identical, implying that conformational changes at the TCR-peptide-MHC binding interface occur after an initial permissive antigen contact. These findings have implications for the rational design of vaccines targeting viruses with unstable genomes. Hide abstract

Ho LP, Urban BC, Jones L, Ogg GS, McMichael AJ. 2004. CD4(-)CD8alphaalpha subset of CD1d-restricted NKT cells controls T cell expansion. J Immunol, 172 (12), pp. 7350-7358. Read abstract

Valpha24 invariant (Valpha24i) CD1d-restricted NKT cells are widely regarded to have immune regulatory properties. They are known to have a role in preventing autoimmune diseases and are involved in optimally mounted immune responses to pathogens and tumor cells. We were interested in understanding how these cells provide protection in autoimmune diseases. We first observed, using EBV/MHC I tetrameric complexes, that expansion of Ag-specific cells in human PBMCs was reduced when CD1d-restricted NKT cells were concomitantly activated. This was accompanied by an increase in a CD4(-)CD8alphaalpha(+) subset of Valpha24i NKT cells. To delineate if a specific subset of NKT cells was responsible for this effect, we generated different subsets of human CD4(-) and CD4(+) Valpha24i NKT clones and demonstrate that a CD4(-)CD8alphaalpha(+) subset with highly efficient cytolytic ability was unique among the clones in being able to suppress the proliferation and expansion of activated T cells in vitro. Activated clones were able to kill CD1d-bearing dendritic or target cells. We suggest that one mechanism by which CD1d-restricted NKT cells can exert a regulatory role is by containing the proliferation of activated T cells, possibly through timely lysis of APCs or activated T cells bearing CD1d. Hide abstract

Stewart-Jones GB, McMichael AJ, Bell JI, Stuart DI, Jones EY. 2003. A structural basis for immunodominant human T cell receptor recognition. Nat Immunol, 4 (7), pp. 657-663. Read abstract | Read more

The anti-influenza CD8+ T cell response in HLA-A2-positive adults is almost exclusively directed at residues 58-66 of the virus matrix protein (MP(58-66)). V(beta)17V(alpha)10.2 T cell receptors (TCRs) containing a conserved arginine-serine-serine sequence in complementarity determining region 3 (CDR3) of the V(beta) segment dominate this response. To investigate the molecular basis of immunodominant selection in an outbred population, we have determined the crystal structure of V(beta)17V(alpha)10.2 in complex with MP(58-66)-HLA-A2 at a resolution of 1.4 A. We show that, whereas the TCR typically fits over an exposed side chain of the peptide, in this structure MP(58-66) exposes only main chain atoms. This distinctive orientation of V(beta)17V(alpha)10.2, which is almost orthogonal to the peptide-binding groove of HLA-A2, facilitates insertion of the conserved arginine in V(beta) CDR3 into a notch in the surface of MP(58-66)-HLA-A2. This previously unknown binding mode underlies the immunodominant T cell response. Hide abstract

Simmons A, Aluvihare V, McMichael A. 2001. Nef triggers a transcriptional program in T cells imitating single-signal T cell activation and inducing HIV virulence mediators. Immunity, 14 (6), pp. 763-777. Read abstract | Read more

Gene expression profiling was used to explore the role of Nef in HIV. Nef induces a transcriptional program in T cells that is 97% identical to that of anti-CD3 T cell activation. This program is inhibited in the presence of cyclosporin. A requirement for TCR zeta and ZAP-70 is demonstrated for formation of the complete profile. Among eight factors particular to the anti-CD3 activation profile are IL16 and YY1, negative regulators of HIV transcription. In contrast, Nef exclusively upregulates factors positively regulating HIV, including Tat-SF1, U1 SNRNP, and IRF-2. New genes associated with Nef include CDK9, the induction of which enhances Tat function. Thus, Nef acts as a master switch early in the viral life cycle, forcing an environment conducive to dynamic viral production. Hide abstract

Kaul R, Dong T, Plummer FA, Kimani J, Rostron T, Kiama P, Njagi E, Irungu E et al. 2001. CD8(+) lymphocytes respond to different HIV epitopes in seronegative and infected subjects. J Clin Invest, 107 (10), pp. 1303-1310. Read abstract | Read more

HIV-1-specific cytotoxic T-lymphocyte (CTL) responses have been detected at a low frequency in many HIV-1-exposed, persistently seronegative (HEPS) subjects. However, it is unclear how CTLs could protect against HIV acquisition in HEPS subjects, when high levels of circulating CTL fail to prevent disease progression in most seropositive subjects. To address this issue we studied CD8(+) lymphocyte responses to a panel of HIV-1 CTL epitopes in 91 HEPS and 87 HIV-1-infected Nairobi sex workers. HIV-specific responses in seropositive women focused strongly on epitopes rarely or never recognized in HEPS subjects, who targeted epitopes that were subdominant or unrecognized in infected women. These differences in epitope specificity were restricted by only those HLA class I alleles that are associated with a reduced risk of HIV-1 infection in this cohort. Late seroconversion in HEPS donors was associated with a switch in epitope specificity and/or immunodominance to those epitopes preferentially recognized by HIV-1-infected women. The likelihood of detecting HIV-1-specific responses in HEPS women increased with the duration of viral exposure, suggesting that HIV-1-specific CD8(+) responses are acquired over time. The association between differential recognition of distinct CTL epitopes and protection from HIV-1 infection may have significant implications for vaccine design. Hide abstract

HIV-1 control by CD8 T cell responses targeting unconventional epitopes

There is a key unmet need in the HIV vaccine field for immunogens that elicit potent cellular immune responses capable of controlling virus replication early after infection occurs, to complement the protection afforded by neutralizing antibodies against virus transmission. During HIV-1 infection CD8 T cells play a key role both in initial containment of viraemia and in subsequent virus control. However, the CD8 T cell response induced in most HIV-1-infected individuals fails to contain virus ...

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Identification of peptides that drive autoimmunity using MHC yeast display platforms

The link between Ankylosing Spondylitis (AS)/Reactive Arthritis (ReA), two forms of inflammatory arthritis, and HLA-B*27 has been recognised for 40 years, but the pathogenic role played by this disease-associated MHC class I protein is not understood.   Various theories have been proposed, including those associating the unusual biology of HLA-B*27 with the overproduction of abnormal protein forms that contribute to inflammatory responses.  However, the original, ‘arthritogenic peptide’ model ...

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The dynamics of activating and inhibitory NK cell receptors at the cell-surface

Natural Killer (NK) cells are innate immune lymphocytes that rapidly destroy virally infected and malignant cells, and constitute major players in the early fight against disease.  Through ‘cross-talk’ with dendritic cells, monocytes and T lymphocytes, they also act as key immune modulators and influence long-term immunity in vivo.  NK cells primarily gauge abnormalities through the loss of cell-surface proteins known as MHC class I proteins on infected/tumour cells - this information is ...

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The impact of IFTIM3 genetic variation on Influenza virus infection, immune responses and disease outcome

Interferon inducible transmembrane 3 (IFITM3) protein is a virus restriction factor mediating cellular resistance to influenza viruses and other viruses. However, the role of IFTIM3 in antiviral immunity is largely unknown. Everitt et al (1) that showed the severity of influenza virus infection was increased in IFITM3 knock out mice compared to wild type animals. They also showed that In northern European patients infected and hospitalized with seasonal influenza or pandemic influenza ...

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Type 1 interferon-mediated control of HIV-1 replication early after transmission

The course of human immunodeficiency virus type 1 (HIV-1) infection is shaped by interactions that occur between the virus and host immune system during the acute phase of infection. Early virus-immune system interactions determine i. whether the transmitted virus is eliminated at initial mucosal infection sites or establishes expanding foci of infection and disseminates; ii. the magnitude of the ensuing acute burst of systemic virus replication; and iii. the efficiency of control of virus ...

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