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Immunotherapy is a treatment that boosts or manipulates the immune system to fight diseases, including cancer. For instance, by stimulating an immune response through vaccinations against viruses that cause cancers, like hepatitis B virus and human papillomavirus, these diseases can be prevented. Nonetheless, some cancer cells can avoid the immune system due to their rapid mutation and division. The immune response to many cancers involves three phases: elimination, equilibrium, and escape.
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Molecular Insights into Tumor Immunogenicity.

Irini Doytchinova1, Stanislav Sotirov1, Ivan Dimitrov1

  • 1Drug Design and Bioinformatics Lab, Faculty of Pharmacy, Medical University of Sofia, Dunav St. 2, 1000 Sofia, Bulgaria.

Current Issues in Molecular Biology
|August 27, 2025
PubMed
Summary

Understanding tumor immunogenicity requires identifying T-cell epitopes. This study reveals that specific amino acid patterns in the central peptide region are crucial for T-cell receptor (TCR) binding and immune response, aiding in cancer vaccine development.

Keywords:
HLA class I bindersT-cell epitopesTCR-based immunotherapiesimmunogenicitymolecular dynamics simulationsneoantigen predictionvaccine design

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Area of Science:

  • Immunology
  • Structural Biology
  • Computational Biology

Background:

  • Tumor immunogenicity relies on peptide interactions with HLA molecules and T-cell receptors (TCRs).
  • Not all HLA-binding peptides trigger T-cell responses, indicating a need to differentiate immunogenic epitopes from non-immunogenic binders.

Purpose of the Study:

  • To identify molecular features distinguishing immunogenic T-cell epitopes from non-immunogenic HLA binders.
  • To provide structural insights into TCR-peptide-HLA interactions for improved neoantigen prediction and immunotherapy design.

Main Methods:

  • Analysis of two nonamer peptide datasets (38 T-cell epitopes, 144 non-epitopes) using sequence logo models.
  • Molecular dynamics (MD) simulations of TCR-peptide-HLA complexes to assess interaction stability and dynamics.
  • Comparative analysis of amino acid preferences at central peptide positions (p4-p8).

Main Results:

  • Sequence logos showed distinct amino acid preferences at central positions (p4-p8) for T-cell epitopes, absent in non-epitopes.
  • MD simulations revealed the T-cell epitope formed a more stable and flexible TCR complex, supporting an induced-fit mechanism.
  • The immunogenic epitope established broader, longer-lasting hydrogen and π interactions at p4-p8, unlike the non-epitope which engaged the TCR at fewer positions.

Conclusions:

  • The central region of a peptide plays a critical role in TCR engagement and immune recognition.
  • Structural insights gained can enhance neoantigen prediction, cancer vaccine design, and TCR-based immunotherapies.