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Updated: Apr 17, 2026
A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes
Published on: March 25, 2014
Expitope: a web server for epitope expression
Kerstin Haase1, Silke Raffegerst2, Dolores J Schendel2
1Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia.
Motivation:
Adoptive T cell therapies based on introduction of new T cell receptors (TCRs) into patient recipient T cells is a promising new treatment for various kinds of cancers. A major challenge, however, is the choice of target antigens. If an engineered TCR can cross-react with self-antigens in healthy tissue, the side-effects can be devastating. We present the first web server for assessing epitope sharing when designing new potential lead targets. We enable the users to find all known proteins containing their peptide of interest. The web server returns not only exact matches, but also approximate ones, allowing a number of mismatches of the users choice. For the identified candidate proteins the expression values in various healthy tissues, representing all vital human organs, are extracted from RNA Sequencing (RNA-Seq) data as well as from some cancer tissues as control. All results are returned to the user sorted by a score, which is calculated using well-established methods and tools for immunological predictions. It depends on the probability that the epitope is created by proteasomal cleavage and its affinities to the transporter associated with antigen processing and the major histocompatibility complex class I alleles. With this framework, we hope to provide a helpful tool to exclude potential cross-reactivity in the early stage of TCR selection for use in design of adoptive T cell immunotherapy.
Availability And Implementation:
The Expitope web server can be accessed via http://webclu.bio.wzw.tum.de/expitope.
Insights
Designing adoptive T cell therapies requires careful antigen selection to avoid self-antigen reactivity. The Expitope web server identifies potential epitope sharing in target antigens, aiding in the early selection of safe T cell receptors (TCRs).
Area of Science:
- Immunology
- Bioinformatics
- Cancer Therapy
Background:
- Adoptive T cell therapies using engineered T cell receptors (TCRs) show promise for cancer treatment.
- A critical challenge is selecting target antigens to prevent devastating side-effects from self-antigen cross-reactivity.
Purpose of the Study:
- To present the first web server, Expitope, for assessing epitope sharing in potential cancer immunotherapy targets.
- To provide a tool for early-stage exclusion of cross-reactive antigens during TCR design.
Main Methods:
- The Expitope web server identifies exact and approximate matches for user-provided peptides within known proteins.
- It analyzes RNA sequencing data to assess protein expression in healthy and cancer tissues.
- Results are scored based on predicted proteasomal cleavage, transporter associated with antigen processing (TAP) affinity, and MHC class I allele binding.
Main Results:
- The server finds all known proteins containing a user's peptide of interest, including near matches.
- Expression levels in various human tissues and cancer types are provided.
- Results are ranked by a comprehensive immunological prediction score.
Conclusions:
- Expitope serves as a valuable tool for researchers designing adoptive T cell immunotherapies.
- It facilitates the exclusion of potentially cross-reactive epitopes early in the TCR selection process.
- This aids in developing safer and more effective cancer treatments.
