Direct identification of HLA-presented CD8 T cell epitopes from transmitted founder HIV-1 variants

doi:10.1002/pmic.202100142

. 2021 Sep;21(17-18):e2100142.

doi: 10.1002/pmic.202100142. Epub 2021 Aug 1.

Direct identification of HLA-presented CD8 T cell epitopes from transmitted founder HIV-1 variants

Jonathan Hare^{1

2}, Gladys Macharia^{1

3}, Ling Yue⁴, Claire L Streatfield^{1

3}, Eric Hunter⁴, Anthony Purcell⁵, Nicola Ternette⁶, Jill Gilmour³

Affiliations

¹ IAVI Human Immunology Laboratory, Imperial College London, London, UK.
² IAVI, New York, New York, USA.
³ Department of Infectious Disease, Imperial College London, London, UK.
⁴ Emory Vaccine Center, Emory University, Atlanta, Georgia, USA.
⁵ Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
⁶ The Jenner Institute, University of Oxford, Oxford, UK.

PMID: 34275180
DOI: 10.1002/pmic.202100142

Direct identification of HLA-presented CD8 T cell epitopes from transmitted founder HIV-1 variants

Jonathan Hare et al. Proteomics. 2021 Sep.

. 2021 Sep;21(17-18):e2100142.

doi: 10.1002/pmic.202100142. Epub 2021 Aug 1.

Authors

Jonathan Hare^{1

2}, Gladys Macharia^{1

3}, Ling Yue⁴, Claire L Streatfield^{1

3}, Eric Hunter⁴, Anthony Purcell⁵, Nicola Ternette⁶, Jill Gilmour³

Affiliations

¹ IAVI Human Immunology Laboratory, Imperial College London, London, UK.
² IAVI, New York, New York, USA.
³ Department of Infectious Disease, Imperial College London, London, UK.
⁴ Emory Vaccine Center, Emory University, Atlanta, Georgia, USA.
⁵ Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
⁶ The Jenner Institute, University of Oxford, Oxford, UK.

PMID: 34275180
DOI: 10.1002/pmic.202100142

Abstract

Cytotoxic T lymphocytes (CTLs) are a critical arm of the immune response to viral infections. The activation and expansion of antigen specific CTL requires recognition of peptide antigens presented on class I major histocompatibility complex molecules (MHC-1) of infected cells. Methods to identify presented peptide antigens that do not rely on the pre-existence of antigen specific CTL are critical to the development of new vaccines. We infected activated CD4+ T cells with two HIV-1 transmitted founder (TF) isolates and used high-resolution mass spectrometry (MS) to identify HIV peptides bound on MHC-1. Using this approach, we identified 14 MHC-1 bound peptides from across the two TF isolates. Assessment of predicted binding thresholds revealed good association of the identified peptides to the shared HLA alleles between the HIV+ donors and the naïve PBMC sample with three peptides identified through peptide sequencing inducing a CD8 T-cell response (p < 0.05). Direct infection of naïve CD4 cells by HIV TF isolates and sequencing of MHC-I presented peptides by HPLC-MS/MS enables identification of novel peptides that may be missed by alternative epitope mapping strategies and can provide valuable insight in to the first peptides presented by an HIV-infected CD4 cell in the first few days post infection.

Keywords: biomedicine; immunoproteomics; infectious diseases; mass spectrometry-LC-MS/MS; technology.

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[1] Appay, V., Papagno, L., Spina, C. A., Hansasuta, P., King, A., Jones, L., Ogg, G. S., Little, S., Mcmichael, A. J., Richman, D. D., & Rowland-Jones, S. L. (2002). Dynamics of T cell responses in HIV infection. Journal of Immunology, 168(7), 3660-3666.

[2] Appay, V., Papagno, L., Spina, C. A., Hansasuta, P., King, A., Jones, L., Ogg, G. S., Little, S., Mcmichael, A. J., Richman, D. D., & Rowland-Jones, S. L. (2002). Dynamics of T cell responses in HIV infection. Journal of Immunology, 168(7), 3660-3666.

[3] Goonetilleke, N., Liu, M. K. P., Salazar-Gonzalez, J. F., Ferrari, G., Giorgi, E., Ganusov, V. V., Keele, B. F., Learn, G. H., Turnbull, E. L., Salazar, M. G., Weinhold, K. J., Moore, S., Letvin, N., Haynes, B. F., Cohen, M. S., Hraber, P., Bhattacharya, T., Borrow, P., Perelson, A. S., … Mcmichael, A. J. (2009). The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. Journal of Experimental Medicine, 206(6), 1253-1272. https://doi.org/10.1084/jem.20090365

[4] Goonetilleke, N., Liu, M. K. P., Salazar-Gonzalez, J. F., Ferrari, G., Giorgi, E., Ganusov, V. V., Keele, B. F., Learn, G. H., Turnbull, E. L., Salazar, M. G., Weinhold, K. J., Moore, S., Letvin, N., Haynes, B. F., Cohen, M. S., Hraber, P., Bhattacharya, T., Borrow, P., Perelson, A. S., … Mcmichael, A. J. (2009). The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. Journal of Experimental Medicine, 206(6), 1253-1272. https://doi.org/10.1084/jem.20090365

[5] Bosinger S. E., Jochems S. P., Folkner K. A., Hayes T. L., Klatt N. R., & Silvestri G. (2013). Transcriptional profiling of experimental CD8(+) lymphocyte depletion in rhesus macaques infected with simian immunodeficiency virus SIVmac239. Journal of Virology, 87(1), 433-443. https://doi.org/10.1128/jvi.01746-12

[6] Bosinger S. E., Jochems S. P., Folkner K. A., Hayes T. L., Klatt N. R., & Silvestri G. (2013). Transcriptional profiling of experimental CD8(+) lymphocyte depletion in rhesus macaques infected with simian immunodeficiency virus SIVmac239. Journal of Virology, 87(1), 433-443. https://doi.org/10.1128/jvi.01746-12

[7] Pandrea, I., Gaufin, T., Gautam, R., Kristoff, J., Mandell, D., Montefiori, D., Keele, B. F., Ribeiro, R. M., Veazey, R. S., & Apetrei, C. (2011). Functional cure of SIVagm infection in rhesus macaques results in complete recovery of CD4+ T cells and is reverted by CD8+ cell depletion. PLoS Pathogens, 7(8), e1002170. https://doi.org/10.1371/journal.ppat.1002170

[8] Pandrea, I., Gaufin, T., Gautam, R., Kristoff, J., Mandell, D., Montefiori, D., Keele, B. F., Ribeiro, R. M., Veazey, R. S., & Apetrei, C. (2011). Functional cure of SIVagm infection in rhesus macaques results in complete recovery of CD4+ T cells and is reverted by CD8+ cell depletion. PLoS Pathogens, 7(8), e1002170. https://doi.org/10.1371/journal.ppat.1002170

[9] Arunachalam, P. S., Charles, T. P., Joag, V., Bollimpelli, V. S., Scott, M. K. D., Wimmers, F., Burton, S. L., Labranche, C. C., Petitdemange, C., Gangadhara, S., Styles, T. M., Quarnstrom, C. F., Walter, K. A., Ketas, T. J., Legere, T., Jagadeesh Reddy, P. B., Kasturi, S. P., Tsai, A., Yeung, B. Z., … Pulendran, B. (2020). T cell-inducing vaccine durably prevents mucosal SHIV infection even with lower neutralizing antibody titers. Nature Medicine, 26(6), 932-940. https://doi.org/10.1038/s41591-020-0858-8

[10] Arunachalam, P. S., Charles, T. P., Joag, V., Bollimpelli, V. S., Scott, M. K. D., Wimmers, F., Burton, S. L., Labranche, C. C., Petitdemange, C., Gangadhara, S., Styles, T. M., Quarnstrom, C. F., Walter, K. A., Ketas, T. J., Legere, T., Jagadeesh Reddy, P. B., Kasturi, S. P., Tsai, A., Yeung, B. Z., … Pulendran, B. (2020). T cell-inducing vaccine durably prevents mucosal SHIV infection even with lower neutralizing antibody titers. Nature Medicine, 26(6), 932-940. https://doi.org/10.1038/s41591-020-0858-8

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Direct identification of HLA-presented CD8 T cell epitopes from transmitted founder HIV-1 variants

Affiliations

Direct identification of HLA-presented CD8 T cell epitopes from transmitted founder HIV-1 variants

Authors

Affiliations

Abstract

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References

REFERENCES

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LinkOut - more resources

Full Text Sources

Research Materials

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