Combinatorial tetramer staining and mass cytometry analysis facilitate T-cell epitope mapping and characterization

Newell, Evan W.; Sigal, Natalia; Nair, Nitya; Kidd, Brian; Greenberg, Harry B.; Davis, Mark M.

doi:10.1038/nbt.2593

Cited by 263 publications

(249 citation statements)

References 35 publications

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“…Recent work by Rosenberg and colleagues (38) and by us (39) has demonstrated how cancer exome sequencing data can be used to reveal T cell responses against patient-specific neoantigens in humans, and how such responses can be influenced by immunotherapy (39). The development of pMHC-based monitoring technology for large sets of HLA subtypes will be of substantial importance for such personalized immunomonitoring, either by the flow cytometry-based approaches used in this study, or by the high-throughput MHC multimer-based mass cytometry recently developed by Newell and colleagues (40).…”

Section: Discussionmentioning

confidence: 94%

HLA Micropolymorphisms Strongly Affect Peptide–MHC Multimer–Based Monitoring of Antigen-Specific CD8+ T Cell Responses

Buuren

Dijkgraaf

Linnemann

et al. 2014

The Journal of Immunology

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Peptide–MHC (pMHC) multimers have become one of the most widely used tools to measure Ag-specific T cell responses in humans. With the aim of understanding the requirements for pMHC-based personalized immunomonitoring, in which individuals expressing subtypes of the commonly studied HLA alleles are encountered, we assessed how the ability to detect Ag-specific T cells for a given peptide is affected by micropolymorphic differences between HLA subtypes. First, analysis of a set of 10 HLA-A*02:01–restricted T cell clones demonstrated that staining with pMHC multimers of seven distinct subtypes of the HLA-A*02 allele group was highly variable and not predicted by sequence homology. Second, to analyze the effect of minor sequence variation in a clinical setting, we screened tumor-infiltrating lymphocytes of an HLA-A*02:06 melanoma patient with either subtype-matched or HLA-A*02:01 multimers loaded with 145 different melanoma-associated Ags. This revealed that of the four HLA-A*02:06–restricted melanoma-associated T cell responses observed in this patient, two responses were underestimated and one was overlooked when using subtype-mismatched pMHC multimer collections. To our knowledge, these data provide the first demonstration of the strong effect of minor sequence variation on pMHC-based personalized immunomonitoring, and they provide tools to prevent this issue for common variants within the HLA-A*02 allele group.

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Section: Discussionmentioning

confidence: 94%

HLA Micropolymorphisms Strongly Affect Peptide–MHC Multimer–Based Monitoring of Antigen-Specific CD8+ T Cell Responses

Buuren

Dijkgraaf

Linnemann

et al. 2014

The Journal of Immunology

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“…Identification of the optimal TEAD1 epitope, which was not present in the initial screening assays carried out with TILs from patient 3466, illustrates one of the problems encountered using current peptide prediction algorithms. Further improvements could take advantage of advanced tetramer screening methods such as combinatorial tetramer staining and mass cytometric analysis to facilitate characterization of the mutated epitopes (23)(24)(25). Additional conditional MHC ligands (26) for less frequent HLA alleles are also needed to expand the use of this approach to a wider patient population.…”

Section: Discussionmentioning

confidence: 99%

Isolation of neoantigen-specific T cells from tumor and peripheral lymphocytes

Cohen

Gartner

Horovitz-Fried

et al. 2015

Journal of Clinical Investigation

335

275

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“…Given that most experiments use polyclonal CD4 + T cells to differentiate T cells into Treg cells and other T-cell subpopulations, most of these experiments might start with a mix of pre-nTreg and so-called Tconv cells and resulting Treg cells might resemble a mix of FoxP3-induced Treg cells. This would be in analogy to the CD8 + T-cell compartment, which had been shown to be more complex than previously appreciated (40,41). In light of the data presented here, we hypothesize that other T-cell subsets might exist within the plenitude of Tconv cell population with a bias in their differentiation capacity toward any T-cell lineage.…”

Section: Foxp3mentioning

confidence: 49%

Nuclear transfer nTreg model reveals fate-determining TCR-β and novel peripheral nTreg precursors

Ku¹,

Chang²,

Hernández³

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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To study the development and function of "natural-arising" T regulatory (nTreg) cells, we developed a novel nTreg model on pure nonobese diabetic background using epigenetic reprogramming via somatic cell nuclear transfer. On RAG1-deficient background, we found that monoclonal FoxP3 + CD4 + Treg cells developed in the thymus in the absence of other T cells. Adoptive transfer experiments revealed that the thymic niche is not a limiting factor in nTreg development. In addition, we showed that the T-cell receptor (TCR) β-chain of our nTreg model was not only sufficient to bias T-cell development toward the CD4 lineage, but we also demonstrated that this TCR β-chain was able to provide stronger TCR signals. This TCR-β-driven mechanism would thus unify former per se contradicting hypotheses of TCR-dependent and -independent nTreg development. Strikingly, peripheral FoxP3 − CD4 + T cells expressing the same TCR as this somatic cell nuclear transfer nTreg model had a reduced capability to differentiate into Th1 cells but were poised to differentiate better into induced nTreg cells, both in vitro and in vivo, representing a novel peripheral precursor subset of nTreg cells to which we refer to as pre-nTreg cells. ). The development and selection of nTreg cells in the thymus has been the subject of scientific debates for decades, and two contradicting hypotheses have been formulated. Although one hypothesis emphasized the development of nTreg cells in a T-cell receptor (TCR)-dependent manner, the other hypothesis postulated a TCR-independent mechanism. The TCR-dependent development is supported by the observation that TCR transgenic models generated from non-Treg cells did not possess any nTreg cells (7). In line with the TCR-dependent hypothesis is the notion that Treg cells developed in non-Treg TCR transgenic models only when the cognate antigen was expressed in the thymus (8-10). The TCR-independent hypothesis was proposed based on the observation that nTreg development was favored in a subset of CD4 − CD8 − double-negative (DN) cells before the expression of a full TCR on the surface, and that development of Treg cells was less affected than that of conventional CD4+ T cells in pre-TCR-α −/− (pTα) mice (11,12). Given that the pTα, together with TCR-β, is expressed as pre-TCR at the CD4 CD8 DN stage 3 (DN3) before selection at the CD4 CD8 double-positive (DP) stage, a TCR-independent Treg development was indicated. In addition, although some studies investigating the TCR repertoire of conventional T cells (Tconv) and Treg cells demonstrated a partial overlap in support of the TCR-independent hypothesis, other studies reported no gross similarity of the TCR repertoire, in line with a TCR-dependent development (13-15).TCR transgenic mice have been valuable tools in better understanding the role of T cells in health and disease. Several mouse models had been made to study the development and function of nTreg cells. First studies used existing non-Treg TCR transgenic mice and expressed the cognate antigen in the thymus...

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Combinatorial tetramer staining and mass cytometry analysis facilitate T-cell epitope mapping and characterization

Cited by 263 publications

References 35 publications

HLA Micropolymorphisms Strongly Affect Peptide–MHC Multimer–Based Monitoring of Antigen-Specific CD8+ T Cell Responses

HLA Micropolymorphisms Strongly Affect Peptide–MHC Multimer–Based Monitoring of Antigen-Specific CD8+ T Cell Responses

Isolation of neoantigen-specific T cells from tumor and peripheral lymphocytes

Nuclear transfer nTreg model reveals fate-determining TCR-β and novel peripheral nTreg precursors

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