Literature

Key publications of UV induced peptide exchange and Combinatorial Coding

UV = UV-cleavable peptide-MHC exchange

CC = application of combinatorial (color) coded MHC complexes allowing evaluation of more antigen specificities than single color available in FACS

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Axmann, M et al.. (2015) Measuring TCR-pMHC Binding In Situ using a FRET-based Microscopy Assay. J. Vis. Exp. (104), e53157, doi:10.3791/53157.

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Cohen, CJ et al. (2015) Isolation of neoantigen-specific T cells from tumor and peripheral lymphocytes. J Clin Invest 125:3981-3991.

Isolation of mutation-reactive T cells from patients’ peripheral blood prior to immune therapy. Authors point out potential for designing personalized immunotherapies to treat patients with advanced cancer

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Frøsig, TM et al. (2015) Design and validation of conditional ligands for HLA-B*08:01, HLA-B*15:01, HLA-B*35:01, and HLA-B*44:05. Cytometry Part A 87, 10:  967–975

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Rizvi, NA et al. (2015) Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science 348:124-128.

112 candidate neoantigens were synthesized and HLA-multimers containing these peptides,  produced by micro-scale parallel UV-induced peptide exchange reactions, were applied to monitor the effect of anti-PD-1 therapy on cytotoxic T cell populations.

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Frøsig, TM et al. (2015) Broadening the repertoire of melanoma-associated T-cell epitopes. Cancer Immunol Immunother 64: 609-620.

This study identified 127 MHC ligands and analyzed the T-cell responses against these ligands in peripheral blood from 39 melanoma patients and 10 healthy donors.

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Hadrup, SR et al. (2015) Cryopreservation of MHC multimers: Recommendations for quality assurance in detection of antigen specific T cells. Cytometry Part A 87A: 37-48.

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Ziegler, S et al. (2014) Impact of sequence variation in a dominant HLA-A*02-restricted epitope in hepatitis C virus on priming and cross-reactivity of CD8+ T cells. J Virol 88: 11080-11090.

The results have important implications for vaccine design against highly variable pathogens and suggest that evidence-based selection of the vaccine antigen sequence may improve immunogenicity.

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Van Buuren, MM et al. (2014) HLA micropolymorphisms strongly effect peptide-MHC multimer-based monitoring of antigen-specific CD8+ T cell responses. J Immunol 192: 641-648

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Gang, AO et al. (2014) 5-Azacytidine treatment sensitizes tumor cells to T-cell mediated cytotoxicity and modulates NK cells in patients with myeloid malignancies. Blood Cancer J 4: e197 doi: 10.1038/bcj.2014.14.

The frequency of MHC-multimer-specific T cells was determined by flow cytometry using UV-exchange and combinatorial coding. T-cell responses against a large panel of cancer-testis antigens were detected before treatment, and these responses were further induced upon initiation of treatment. The data support a strategy for combining 5-Azacytidine treatment with immune therapy for potential clinical benefit.

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Kvistborg, P et al. (2014) Anti-CTLA-4 therapy broadens the melanoma-reactive CD8+ T cell response. Sci Transl Med 6: 254ra128.

Using a combination ultraviolet (UV)–induced peptide exchange and peptide–major histocompatibility complex (pMHC) combinatorial coding, the authors monitored immune reactivity against a panel of 145 melanoma-associated epitopes in a cohort of patients receiving anti–CTLA-4 treatment. Results provide evidence for anti–CTLA-4 therapy–enhanced T cell priming as a component of the clinical mode of action.

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Van Rooij, N et al. (2013) Tumor exome analysis reveals neoantigen-specific T-cell reactivity in an ipilimumab-responsive melanoma. J Clin Oncol 31: doi:10.1200/JCO.2012.47.7521.

HLA multimers containing selected ligands were produced by micro-scale parallel UV-induced peptide exchange. predicted T-cell epitopes were analyzed by a multiplexed major histocompatibility complex (MHC) multimer staining strategy. The authors show how autologous cancer exome data can be used to reveal T-cell responses against patient-specific neoantigens in humans.

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Linnemann, C et al. (2013) High-throughput identification of antigen-specific TCRs by TCR gene capture. Nat Med 19: 1534-1541.

Patient samples were used to screen for T cells specific for any of 145 melanoma-associated antigens by MHC multimer combinatorial coding analyses. The authors demonstrate the ability to identify tumor-reactive TCRs within intratumoral T cell subsets without knowledge of antigen specificities, which may be the first step toward the development of autologous TCR gene therapy to target patient-specific neoantigens in human cancer

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Lin, L et al. (2013) Hierarchical Bayesian mixture modelling for antigen-specific T-cell subtyping in combinatorially encoded flow cytometry studies. Stat Appl Genet Mol Biol 12: 309-331.

Describes statistical methods to automate the detection of antigen-specific T-cells using data sets from an experimental study of antigen-specific T-cell subtyping using combinatorially encoded assays in human blood samples. Illustrates that conventional methods would require the collection and analysis of large (and infeasible) volumes of peripheral blood from each patient, and the sample sparing advantages of combinatorial encoding are key to a feasible screening strategy.

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Munir, S et al. (2013) HLA-restricted CTL that are specific for the immune checkpoint ligand PD-L1 occur with high frequency in cancer patients. Cancer Res 73: 1764-1776.

The affinity of peptides to the HLA complex were analysed using UV-exchange ELISA assay. Subsequently, tetramers coupled with PE and APCs were prepared. The data presented suggest that natural CD8 reactivity toward PD-L1 exist.

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Chang, CXL et al. (2013) Conditional ligands for Asian HLA variants facilitate the definition of CD8+ T-cell responses in acute and chronic viral diseases. Eur J Immunol 43: 1109-1120.

Description of 30 novel irradiation-sensitive ligands, specifically targeting South East Asian populations. Fluorescently labeled HLA tetramers for EBV, human cytomegalovirus, HBV, DENV, and influenza A virus epitopes were generated by UV-exchange and could detect antigen-specific CD8+ T-cell responses against these viruses.

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Larsen, SK et al. (2013) Functional characterization of Foxp3-specific spontaneous immune responses. Leukemia 27: 2332-2340.

The affinity of peptides to the HLA complex were analyzed using UV-exchange ELISA assay. Subsequently, tetramers coupled with PE and APCs were prepared.

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Munir, S et al. (2012) Characterization of T-cell responses against IκBα in cancer patients. OncoImmunology 1: 1290-1296.

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Hadrup, SR (2012) The antigen specific composition of melanoma tumor infiltrating lymphocytes? OncoImmunology 1: 935-936.

Screening of peptide-specific T cell responses was conducted by MHC multimers, generated by peptide exchange from conditional ligand-HLA complexes and combinatorially encoded with different fluorescence molecules to generate unique two-colour codes allowing parallel detection of large numbers of different antigen specific T cells.

Conclusion: high-throughput sequencing and detection of T-cell responses will allow the identification of patient specific mutations and the recognition of these by patients TILs.

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Kvistborg, P et al. (2012) TIL therapy broadens the tumor-reactive CD8+T cell compartment in melanoma patients. OncoImmunology 1: 409-418.

Specific peptide-MHC complexes were generated by UV-induced ligand exchange. Multimers were generated using a total of eight different fluorescent streptavidin conjugates

The results establish the value of high throughput monitoring for the analysis of immuno-active therapeutics and suggest that the clinical efficacy of TIL therapy can be enhanced by the preparation of more defined tumor-reactive T cell products.

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UV-CC / CT: Andersen, RS et al. (2012) Dissection of T-cell antigen specificity in human melanoma. Cancer Res. 72: 1642-1650.

Specific pHLA complexes were generated with the MHC peptide exchange technology. Multimers were generated with 8 different fluorescent-streptavidin conjugates to obtain 27 unique colour combinations.

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Andersen, RS et al. (2012) Parallel detection of antigen-specific T cell responses by combinatorial encoding of MHC multimers. Nat Protocols 7: 891-902.

By the use of combinatorial encoding, a large number of different T cell populations was detected in a single sample. Authors indicated the method can be used for T cell epitope mapping and for monitoring of CD8 + immune responses during cancer and infectious disease or after immunotherapy. One panel of 28 combinatorially encoded MHC multimers was prepared in 4 h. Staining and detection took a further 3 h.

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Ung W et al. (2011) Discovery of low-affinity preproinsulin epitopes and detection of autoreactive CD8 T-cells using combinatorial MHC multimers. J Autoimmunity 37: 151-159.

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Hombrink, P et al. (2011) High-throughput identification of potential minor histocompatibility antigens by MHC tetramer-based screening: feasibility and limitations. Plos ONE 6: e22523.

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Broen, K et al. (2011) Concurrent detection of circulating minor histocompatibility antigen-specific CD8+ T cells in SCT recipients by combinatorial encoding MHC multimers. PloS ONE 6: e21266.

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Brackenridge, S et al. (2011) An early HIV mutation within an HLA-B*57-restricted T cell epitope abrogates binding to the killer inhibitory receptor 3DL1. J Virol 85: 5415-5422.

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Schulte, I et al. (2011) Characterization of CD8+ T cell response in acute and resolved hepatitis A virus infection. J Hepatol 54: 201-208.

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Chew, SL et al. (2011) Stability screening of arrays of major histocompatibility complexes on combinatorially encoded flow cytometry beads. J Biol Chem 286: 28466–28475.

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Velthuis, JH et al. (2010) Simultaneous detection of circulating autoreactive CD8+ T cells specific for different islet cell-associated epitopes using combinatorial MHC-multimers. Diabetes  59: 1721-1730.

Authors show that conventional detection techniques (ELISPOT and HLA tetramers) require many cells and are relatively insensitive, compared to combinatorial MHC multimer technique to simultaneously monitor the presence of HLA-A2 restricted insulin epitopes.

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Hadrup SR and Schumacher TN. (2010) MHC-based detection of antigen-specific CD8+ T cell responses. Cancer Immunol Immunother 59: 1425-1433.

Toebes, M et al. (2009) Generation of peptide MHC class I monomers and multimers through ligand exchange. Curr Protoc Immunol : Chapter 18:Unit 18.16.

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Hadrup, SR et al. (2009) High-throughput T cell epitope discovery through MHC peptide exchange. Methods Mol Biol 524: 383-405.

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Hadrup, SR et al. (2009) Parallel detection of antigen-specific T cell responses by multidimensional encoding of MHC multimers. Nat Methods 6: 520-526.

First paper to demonstrate the feasibility of large-scale screening of human material by analysis of human leukocyte antigen A3–restricted T-cell responses.

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Celie, PH et al. (2009) UV-induced ligand exchange in MHC class I protein crystals. J Am Chem Soc 131: 12298-12304.

UV-induced exchange in crystallant solution.

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Bakker, AH et al. (2008) Conditional MHC class I ligands and peptide exchange technology for the human MHC gene products HLA-A1, -A3, -A11, and -B7. Proc Natl Acad Sci USA 105: 3825-3830.

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Grotenbreg, GM et al. (2008) Discovery of CD8+ T cell epitopes in Chlamydia trachomatis infection through use of caged class I MHC tetramers. Proc Natl Acad Sci USA 105: 3831-3836.

Development of photocleavable epitope that bind H-2Kb and H-2Db with full retention of their structural and functional integrity.

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Gredmark-Russ, S et al. (2008) The CD8 T cell response against murine Gammaherpesvirus 68 is directed toward a broad repertoire of epitopes from both early and late antigens. J Virol 82: 12205–12212.

Screen of 384 H-2Kb- and H-2Db-restricted epitopes.

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Frickel, EM et al. (2008) Parasite stage–specific recognition of endogenous Toxoplasma gondii–derived CD8+ T cell epitopes. J Infectious Diseases 198: 1625-1633.

Screen of 250 T. gondii–specific T cell epitopes.

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Rodenko, B et al. (2006) Generation of peptide–MHC class I complexes through UV-mediated ligand exchange. Nat Protocols 1: 1120-1132.

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Toebes, M et al. (2006) Design and use of conditional MHC class I ligands. Nat Med 12: 246-251.

First paper describing UV-mediated peptide-MHC exchange.

Last edited on: 19 February 2016