Allergen and Epitope Targets of Mouse-Specific T Cell Responses in Allergy and Asthma

Schulten, Véronique; Westernberg, Luise; Birrueta, Giovanni; Sidney, John; Paul, Sinu; Busse, Paula J.; Peters, Bjoern; Sette, Alessandro

doi:10.3389/fimmu.2018.00235

Cited by 22 publications

(60 citation statements)

References 37 publications

(60 reference statements)

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“…The cluster approach produced significant and meaningful clusters for T-cell epitopes derived from rat and mouse allergens. 34 In this instance, the resulting clusters shared high interconnectivity and were smaller in size, so a clear representative/consensus sequence was observed and similarities among the two species were not inflated by the presence of redundancies.…”

Section: Discussionmentioning

confidence: 83%

“…Alternatively, the cluster approach based on connected components, contains sequences with a lower level of identity with respect to the one used as cut‐off, but where no peptide redundancy is observed in each cluster. The cluster approach produced significant and meaningful clusters for T‐cell epitopes derived from rat and mouse allergens . In this instance, the resulting clusters shared high interconnectivity and were smaller in size, so a clear representative/consensus sequence was observed and similarities among the two species were not inflated by the presence of redundancies.…”

Section: Discussionmentioning

confidence: 95%

“…As another demonstration of the peptide‐clustering application we analysed data derived from a study of mouse allergens. To date, one major mouse allergen, Mus m I, has been identified, to which our laboratory has mapped 23 different T‐cell epitopes . A previous study had identified 19 T‐cell epitopes from the major rat allergen, Rat n I, which exhibits significant homology to Mus m I (65% identity, 78% similarity), making these data sets good candidates for cluster analysis.…”

Section: Resultsmentioning

confidence: 99%

“…The rat epitopes are derived from the rat allergen Rat n I, a major urinary protein, and constitute a set of 19 peptides found to be T‐cell‐reactive in rat‐allergic patients . In addition, our group recently identified 23 peptides from the major mouse allergen, Mus m I …”

Section: Methodsmentioning

confidence: 99%

“…33 In addition, our group recently identified 23 peptides from the major mouse allergen, Mus m I. 34…”

Section: Rat and Mouse Allergen Data Setsmentioning

confidence: 99%

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Development of a novel clustering tool for linear peptide sequences

et al. 2018

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SummaryEpitopes identified in large‐scale screens of overlapping peptides often share significant levels of sequence identity, complicating the analysis of epitope‐related data. Clustering algorithms are often used to facilitate these analyses, but available methods are generally insufficient in their capacity to define biologically meaningful epitope clusters in the context of the immune response. To fulfil this need we developed an algorithm that generates epitope clusters based on representative or consensus sequences. This tool allows the user to cluster peptide sequences on the basis of a specified level of identity by selecting among three different method options. These include the ‘clique method’, in which all members of the cluster must share the same minimal level of identity with each other, and the ‘connected graph method’, in which all members of a cluster must share a defined level of identity with at least one other member of the cluster. In cases where it is not possible to define a clear consensus sequence with the connected graph method, a third option provides a novel ‘cluster‐breaking algorithm’ for consensus sequence driven sub‐clustering. Herein we demonstrate the tool's clustering performance and applicability using (i) a selection of dengue virus epitopes for the ‘clique method’, (ii) sets of allergen‐derived peptides from related species for the ‘connected graph method’ and (iii) large data sets of eluted ligand, major histocompatibility complex binding and T‐cell recognition data captured within the Immune Epitope Database (IEDB) with the newly developed ‘cluster‐breaking algorithm’. This novel clustering tool is accessible at http://tools.iedb.org/cluster2/.

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Section: Discussionmentioning

confidence: 83%

Section: Discussionmentioning

confidence: 95%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…33 In addition, our group recently identified 23 peptides from the major mouse allergen, Mus m I. 34…”

Section: Rat and Mouse Allergen Data Setsmentioning

confidence: 99%

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Development of a novel clustering tool for linear peptide sequences

et al. 2018

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Heterogeneity of magnitude, allergen immunodominance, and cytokine polarization of cockroach allergen‐specific T cell responses in allergic sensitized children

Antunes

Sutherland

Schulten

et al. 2021

Clinical & Translational All

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Background Characterization of allergic responses to cockroach (CR), a common aeroallergen associated with asthma, has focused mainly on IgE reactivity, but little is known about T cell responses, particularly in children. We conducted a functional evaluation of CR allergen‐specific T cell reactivity in a cohort of CR allergic children with asthma. Methods Peripheral blood mononuclear cells (PBMCs) were obtained from 71 children, with mild‐to‐moderate asthma who were enrolled in a CR immunotherapy (IT) clinical trial, prior to treatment initiation. PBMC were stimulated with peptide pools derived from 11 CR allergens, and CD4+ T cell responses assessed by intracellular cytokine staining. Results Highly heterogeneous responses in T cell reactivity were observed among participants, both in terms of the magnitude of cytokine response and allergen immunodominance. Reactivity against Bla g 9 and Bla g 5 was most frequent. The phenotype of the T cell response was dominated by IL‐4 production and a Th2 polarized profile in 54.9% of participants, but IFNγ production and Th1 polarization was observed in 25.3% of the participants. The numbers of regulatory CD4+ T cells were also highly variable and the magnitude of effector responses and Th2 polarization were positively correlated with serum IgE levels specific to a clinical CR extract. Conclusions Our results demonstrate that in children with mild‐to‐moderate asthma, CR‐specific T cell responses display a wide range of magnitude, allergen dominance, and polarization. These results will enable examination of whether any of the variables measured are affected by IT and/or are predictive of clinical outcomes.

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The MegaPool Approach to Characterize Adaptive CD4+ and CD8+ T Cell Responses

da Silva Antunes,

Weiskopf,

Sidney

et al. 2023

Current Protocols

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Epitopes recognized by T cells are a collection of short peptide fragments derived from specific antigens or proteins. Immunological research to study T cell responses is hindered by the extreme degree of heterogeneity of epitope targets, which are usually derived from multiple antigens; within a given antigen, hundreds of different T cell epitopes can be recognized, differing from one individual to the next because T cell epitope recognition is restricted by the epitopes’ ability to bind to MHC molecules, which are extremely polymorphic in different individuals. Testing large pools encompassing hundreds of peptides is technically challenging because of logistical considerations regarding solvent‐induced toxicity. To address this issue, we developed the MegaPool (MP) approach based on sequential lyophilization of large numbers of peptides that can be used in a variety of assays to measure T cell responses, including ELISPOT, intracellular cytokine staining, and activation‐induced marker assays, and that has been validated in the study of infectious diseases, allergies, and autoimmunity. Here, we describe the procedures for generating and testing MPs, starting with peptide synthesis and lyophilization, as well as a step‐by‐step guide and recommendations for their handling and experimental usage. Overall, the MP approach is a powerful strategy for studying T cell responses and understanding the immune system's role in health and disease. © 2023 Wiley Periodicals LLC.Basic Protocol 1: Generation of peptide pools (“MegaPools”)Basic Protocol 2: MegaPool testing and quantitation of antigen‐specific T cell responses

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Allergen and Epitope Targets of Mouse-Specific T Cell Responses in Allergy and Asthma

Cited by 22 publications

References 37 publications

Development of a novel clustering tool for linear peptide sequences

Development of a novel clustering tool for linear peptide sequences

Heterogeneity of magnitude, allergen immunodominance, and cytokine polarization of cockroach allergen‐specific T cell responses in allergic sensitized children

The MegaPool Approach to Characterize Adaptive CD4+ and CD8+ T Cell Responses

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